From 2fd1e4bbeffbaeddfda605fdb753ee6b1228653a Mon Sep 17 00:00:00 2001 From: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com> Date: Fri, 15 Dec 2023 09:18:36 +0100 Subject: [PATCH 1/4] Concat: fix using 'move' with a missing conflicting metadata column. (#631) * Concat: fix using 'move' with a missing conflicting metadata column. This commit fixes `TypeError`s when trying to concatenate three or more samples using `--mode move`. The error occurs when one of the samples does not contain the column that does trigger a conflict in the other samples. In mode `move`, the conflicting metadata columns are gathered across the samples and moved to the multidimensional annotation data slot (obsm or varm). The problem is that the sample names are used as the column namnes for the dataframe, but because one or more columns is missing, the number of input samples is differs from the number of columns. * Update CHANGELOG with PR number * Fix test looking at wrong attribute * Revert changing attribute in tests --- CHANGELOG.md | 6 +---- src/dataflow/concat/script.py | 37 ++++++++++++++-------------- src/dataflow/concat/test.py | 45 +++++++++++++++++++++++++++++++---- 3 files changed, 61 insertions(+), 27 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 140d7679fb7..244583a054c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,11 +4,7 @@ * `dataflow/concat`: Fix an issue where joining columns with different datatypes caused `TypeError` (PR #619). -# openpipelines 0.12.2 - -## BUG FIXES - -* `dataflow/concat` and `dataflow/concatenate_h5mu`: Fix an issue where using `--mode move` on samples with non-overlapping features would cause `var_names` to become unaligned to the data (PR #653). +* `dataflow/concatenate_h5mu` and `dataflow/concat`: Fix `TypeError` when using mode 'move' and a column with conflicting metadata does not exist across all samples (PR #631). # openpipelines 0.12.1 diff --git a/src/dataflow/concat/script.py b/src/dataflow/concat/script.py index 83c56806058..0b57ff1f38d 100644 --- a/src/dataflow/concat/script.py +++ b/src/dataflow/concat/script.py @@ -121,20 +121,19 @@ def any_row_contains_duplicate_values(n_processes: int, frame: pd.DataFrame) -> is_duplicated = pool.map(nunique, iter(numpy_array)) return any(is_duplicated) -def concatenate_matrices(n_processes: int, input_ids: tuple[str], matrices: Iterable[pd.DataFrame], align_to: pd.Index | None) \ +def concatenate_matrices(n_processes: int, matrices: dict[str, pd.DataFrame], align_to: pd.Index | None) \ -> tuple[dict[str, pd.DataFrame], pd.DataFrame | None, dict[str, pd.core.dtypes.dtypes.Dtype]]: """ Merge matrices by combining columns that have the same name. Columns that contain conflicting values (e.i. the columns have different values), are not merged, but instead moved to a new dataframe. """ - column_names = set(column_name for var in matrices for column_name in var) + column_names = set(column_name for var in matrices.values() for column_name in var) logger.debug('Trying to concatenate columns: %s.', ",".join(column_names)) if not column_names: return {}, pd.DataFrame(index=align_to) conflicts, concatenated_matrix = \ split_conflicts_and_concatenated_columns(n_processes, - input_ids, matrices, column_names, align_to) @@ -151,8 +150,7 @@ def get_first_non_na_value_vector(df): return pd.Series(numpy_arr.ravel()[flat_index], index=df.index, name=df.columns[0]) def split_conflicts_and_concatenated_columns(n_processes: int, - input_ids: tuple[str], - matrices: Iterable[pd.DataFrame], + matrices: dict[str, pd.DataFrame], column_names: Iterable[str], align_to: pd.Index | None = None) -> \ tuple[dict[str, pd.DataFrame], pd.DataFrame]: @@ -166,14 +164,17 @@ def split_conflicts_and_concatenated_columns(n_processes: int, conflicts = {} concatenated_matrix = [] for column_name in column_names: - columns = [var[column_name] for var in matrices if column_name in var] + columns = {input_id: var[column_name] + for input_id, var in matrices.items() + if column_name in var} assert columns, "Some columns should have been found." - concatenated_columns = pd.concat(columns, axis=1, join="outer", sort=False) + concatenated_columns = pd.concat(columns.values(), axis=1, + join="outer", sort=False) if any_row_contains_duplicate_values(n_processes, concatenated_columns): - concatenated_columns.columns = input_ids + concatenated_columns.columns = columns.keys() # Use the sample id as column name if align_to is not None: concatenated_columns = concatenated_columns.reindex(align_to, copy=False) - conflicts[f'conflict_{column_name}'] = concatenated_columns + conflicts[f'conflict_{column_name}'] = concatenated_columns else: unique_values = get_first_non_na_value_vector(concatenated_columns) concatenated_matrix.append(unique_values) @@ -207,7 +208,7 @@ def cast_to_writeable_dtype(result: pd.DataFrame) -> pd.DataFrame: result[obj_col] = result[obj_col].where(result[obj_col].isna(), result[obj_col].astype(str)).astype('category') return result -def split_conflicts_modalities(n_processes: int, input_ids: tuple[str], samples: Iterable[anndata.AnnData], output: anndata.AnnData) \ +def split_conflicts_modalities(n_processes: int, samples: dict[str, anndata.AnnData], output: anndata.AnnData) \ -> anndata.AnnData: """ Merge .var and .obs matrices of the anndata objects. Columns are merged @@ -217,10 +218,10 @@ def split_conflicts_modalities(n_processes: int, input_ids: tuple[str], samples: """ matrices_to_parse = ("var", "obs") for matrix_name in matrices_to_parse: - matrices = [getattr(sample, matrix_name) for sample in samples] + matrices = {sample_id: getattr(sample, matrix_name) for sample_id, sample in samples.items()} output_index = getattr(output, matrix_name).index align_to = output_index if matrix_name == "var" else None - conflicts, concatenated_matrix = concatenate_matrices(n_processes, input_ids, matrices, align_to) + conflicts, concatenated_matrix = concatenate_matrices(n_processes, matrices, align_to) if concatenated_matrix.empty: concatenated_matrix.index = output_index # Write the conflicts to the output @@ -241,20 +242,20 @@ def concatenate_modality(n_processes: int, mod: str, input_files: Iterable[str | } other_axis_mode_to_apply = concat_modes.get(other_axis_mode, other_axis_mode) - mod_data = [] - for input_file in input_files: + mod_data = {} + for input_id, input_file in zip(input_ids, input_files): try: - mod_data.append(mu.read_h5ad(input_file, mod=mod)) + mod_data[input_id] = mu.read_h5ad(input_file, mod=mod) except KeyError as e: # Modality does not exist for this sample, skip it if f"Unable to open object '{mod}' doesn't exist" not in str(e): raise e pass - check_observations_unique(mod_data) + check_observations_unique(mod_data.values()) - concatenated_data = anndata.concat(mod_data, join='outer', merge=other_axis_mode_to_apply) + concatenated_data = anndata.concat(mod_data.values(), join='outer', merge=other_axis_mode_to_apply) if other_axis_mode == "move": - concatenated_data = split_conflicts_modalities(n_processes, input_ids, mod_data, concatenated_data) + concatenated_data = split_conflicts_modalities(n_processes, mod_data, concatenated_data) return concatenated_data diff --git a/src/dataflow/concat/test.py b/src/dataflow/concat/test.py index 0c9196bbfe4..ca07c7627bd 100644 --- a/src/dataflow/concat/test.py +++ b/src/dataflow/concat/test.py @@ -1,5 +1,4 @@ import mudata as md -import anndata as ad import subprocess from pathlib import Path import pandas as pd @@ -7,6 +6,7 @@ import pytest import re import sys +import uuid import muon ## VIASH START @@ -55,13 +55,22 @@ def mudata_without_genome(tmp_path, request): result.append(new_path) return result + @pytest.fixture -def mudata_copy_with_unique_obs(request): +def make_obs_names_unique(): + def wrapper(mudata): + for mod_data in mudata.mod.values(): + mod_data.obs.index = mod_data.obs.index.map( + lambda index_val: uuid.uuid4().hex + index_val + ) + return wrapper + +@pytest.fixture +def mudata_copy_with_unique_obs(request, make_obs_names_unique): mudata_to_copy = request.param mudata_contents = md.read(mudata_to_copy) copied_contents = mudata_contents.copy() - for mod_data in copied_contents.mod.values(): - mod_data.obs.index = "make_unique_" + mod_data.obs.index + make_obs_names_unique(copied_contents) return mudata_contents, copied_contents @pytest.fixture @@ -321,6 +330,34 @@ def test_concat_dtypes(run_component, copied_mudata_with_extra_annotation_column concatenated_data = md.read("concat.h5mu") concatenated_data.mod['atac'].obs['test'].dtype == expected +@pytest.mark.parametrize("extra_column_annotation_matrix", ["var"]) +@pytest.mark.parametrize("extra_column_value_sample1,extra_column_value_sample2", [("2", "1")]) +@pytest.mark.parametrize("mudata_copy_with_unique_obs", + [input_sample1_file], + indirect=["mudata_copy_with_unique_obs"]) +def test_resolve_annotation_conflict_missing_column(run_component, copied_mudata_with_extra_annotation_column, make_obs_names_unique, tmp_path): + """ + Test using mode 'move' and resolving a conflict in metadata between the samples, + but the metadata column is missing in one of the samples. + """ + tempfile_input1, tempfile_input2 = copied_mudata_with_extra_annotation_column + original_data = md.read_h5mu(input_sample1_file) + make_obs_names_unique(original_data) + original_data_path = tmp_path / f"{uuid.uuid4().hex}.h5mu" + original_data.write_h5mu(original_data_path) + run_component([ + "--input_id", "mouse,human,sample_without_column", + "--input", tempfile_input1, + "--input", tempfile_input2, + "--input", original_data_path, + "--output", "concat.h5mu", + "--other_axis_mode", "move" + ]) + concatenated_data = md.read("concat.h5mu") + assert 'test' not in concatenated_data.mod['atac'].var.columns + assert 'test' not in concatenated_data.mod['atac'].obs.columns + assert 'conflict_test' in concatenated_data.mod['atac'].varm + def test_mode_move(run_component, tmp_path): tempfile_input1 = tmp_path / "input1.h5mu" tempfile_input2 = tmp_path / "input2.h5mu" From 827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f Mon Sep 17 00:00:00 2001 From: DriesSchaumont <5946712+DriesSchaumont@users.noreply.github.com> Date: Thu, 25 Jan 2024 11:12:21 +0100 Subject: [PATCH 2/4] Update CI --- .github/workflows/create-documentation-pr.yml | 4 +- .github/workflows/integration-test.yml | 159 +++------- .github/workflows/main-build.yml | 280 ++++++++++++++++-- .github/workflows/release-build-viash-hub.yml | 18 +- .github/workflows/release-build.yml | 17 +- .github/workflows/viash-test.yml | 5 +- 6 files changed, 320 insertions(+), 163 deletions(-) diff --git a/.github/workflows/create-documentation-pr.yml b/.github/workflows/create-documentation-pr.yml index f3ef7785861..328cf3a3be6 100644 --- a/.github/workflows/create-documentation-pr.yml +++ b/.github/workflows/create-documentation-pr.yml @@ -28,14 +28,14 @@ jobs: uses: viash-io/viash-actions/ns-list@v4 with: platform: docker - src: src format: json + query_namespace: ^(?!workflows) - id: ns_list_workflows uses: viash-io/viash-actions/ns-list@v4 with: - src: workflows format: json + query_namespace: ^workflows - id: set_matrix run: | diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 5258d7a6686..c2d897c0eed 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -1,169 +1,88 @@ name: integration test +concurrency: + group: ${{ github.workflow }} + cancel-in-progress: false on: workflow_dispatch: + inputs: + push_containers: + type: boolean + required: false + default: true + description: Build docker images and push them to the registry schedule: - cron: '33 2 * * *' jobs: - # phase 1 - list: + # Build and create containers + build: + uses: ./.github/workflows/main-build.yml + with: + push_containers: ${{ github.event_name == 'schedule' || inputs.push_containers }} + version: 'integration_build' + target_tag: 'integration_build' + deploy_to_viash_hub: false + deploy_branch: 'integration_build' + secrets: inherit + + # Synchronize S3 Bucket and create cache for per-component runs + sync_s3: env: s3_bucket: s3://openpipelines-data/ runs-on: ubuntu-latest outputs: - component_matrix: ${{ steps.set_matrix.outputs.components }} - workflow_matrix: ${{ steps.set_matrix.outputs.workflows }} cache_key: ${{ steps.cache.outputs.cache_key }} steps: - - uses: actions/checkout@v4 - - - uses: viash-io/viash-actions/setup@v4 - - uses: viash-io/viash-actions/project/sync-and-cache-s3@v4 - id: cache + id: cache with: s3_bucket: $s3_bucket dest_path: resources_test cache_key_prefix: resources_test__ - - name: Remove target folder from .gitignore - run: | - # allow publishing the target folder - sed -i '/^\/target\/$/d' .gitignore - - - uses: viash-io/viash-actions/ns-build@v4 - with: - config_mod: .functionality.version := 'integration_build' - parallel: true - - - name: Deploy to target branch - uses: peaceiris/actions-gh-pages@v3 - with: - github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: . - publish_branch: integration_build - exclude_assets: '' - - - id: ns_list_components - uses: viash-io/viash-actions/ns-list@v4 - with: - platform: docker - src: src - format: json - - - id: ns_list_workflows - uses: viash-io/viash-actions/ns-list@v4 - with: - src: workflows - format: json - - - id: set_matrix - run: | - echo "components=$(jq -c '[ .[] | - { - "name": (.functionality.namespace + (.platforms | map(select(.type == "docker"))[0].namespace_separator) + .functionality.name), - "config": .info.config, - "dir": .info.config | capture("^(?.*\/)").dir - } - ]' ${{ steps.ns_list_components.outputs.output_file }} )" >> $GITHUB_OUTPUT - - echo "workflows=$(jq -c '[ .[] | . as $config | (.functionality.test_resources // [])[] | select(.type == "nextflow_script", .entrypoint) | - { - "name": ($config.functionality.namespace + "/" + $config.functionality.name), - "main_script": (($config.info.config | capture("^(?.*\/)").dir) + "/" + .path), - "entry": .entrypoint, - "config": $config.info.config - } - ] | unique' ${{ steps.ns_list_workflows.outputs.output_file }} )" >> $GITHUB_OUTPUT - - # phase 2 - build: - needs: list - - runs-on: ubuntu-latest - - strategy: - fail-fast: false - matrix: - component: ${{ fromJson(needs.list.outputs.component_matrix) }} - - steps: - # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' - - uses: data-intuitive/reclaim-the-bytes@v2 - - - uses: actions/checkout@v4 - - - uses: viash-io/viash-actions/setup@v4 - - - name: Build container - uses: viash-io/viash-actions/ns-build@v4 - with: - config_mod: .functionality.version := 'integration_build' - setup: build - src: ${{ matrix.component.dir }} - - - name: Login to container registry - uses: docker/login-action@v3 - with: - registry: ghcr.io - username: ${{ secrets.GTHB_USER }} - password: ${{ secrets.GTHB_PAT }} - - - name: Push container - uses: viash-io/viash-actions/ns-build@v4 - with: - config_mod: .functionality.version := 'integration_build' - platform: docker - src: ${{ matrix.component.dir }} - setup: push - - ################################### # phase 3 integration_test: - needs: [ build, list ] - if: "${{ needs.list.outputs.workflow_matrix != '[]' }}" - runs-on: ubuntu-latest + needs: [ build, sync_s3 ] + if: "${{ needs.build.outputs.workflow_matrix != '[]' }}" strategy: fail-fast: false matrix: - component: ${{ fromJson(needs.list.outputs.workflow_matrix) }} + component: ${{ fromJson(needs.build.outputs.workflow_matrix) }} steps: # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' - uses: data-intuitive/reclaim-the-bytes@v2 - + + - name: Keep symlinks as-is + run: | + git config --global core.symlinks true + - uses: actions/checkout@v4 + with: + ref: 'integration_build' - uses: viash-io/viash-actions/setup@v4 - - uses: nf-core/setup-nextflow@v1.3.0 - - # build target dir - # use containers from integration_build branch, hopefully these are available - - name: Build target dir - uses: viash-io/viash-actions/ns-build@v4 - with: - config_mod: ".functionality.version := 'integration_build'" - parallel: true + - uses: nf-core/setup-nextflow@v1.5.0 # use cache - name: Cache resources data - uses: actions/cache@v3 + uses: actions/cache@v4 timeout-minutes: 5 with: path: resources_test - key: ${{ needs.list.outputs.cache_key }} + key: ${{ needs.sync_s3.outputs.cache_key }} fail-on-cache-miss: true - name: Remove unused test resources to save space shell: bash run: | - readarray -t resources < <(viash config view --format json "${{ matrix.component.config }}" | jq -r -c '(.info.config | capture("^(?.*\/)").dir) as $dir | .functionality.test_resources | map(select(.type == "file")) | map($dir + .path) | unique | .[]') + readarray -t resources < <(viash config view --format json "${{ matrix.component.config }}" -c 'del(.functionality.dependencies)' | jq -r -c '(.info.config | capture("^(?.*\/)").dir) as $dir | .functionality.test_resources | map(select(.type == "file")) | map($dir + .path) | unique | .[]') to_not_remove=() for resource in "${resources[@]}"; do if [[ $resource == *"resources_test"* ]]; then @@ -178,7 +97,9 @@ jobs: unset 'to_not_remove[${#to_not_remove[@]}-1]' to_not_remove+=( "(" "${to_not_remove[@]}" ")" "-prune" "-o") fi + echo "Not removing ${to_not_remove[@]}" find ./resources_test/ "${to_not_remove[@]}" -type f -exec rm {} + + tree ./resources_test/ - name: Run integration test timeout-minutes: 60 @@ -189,4 +110,4 @@ jobs: -main-script "${{ matrix.component.main_script }}" \ -entry "${{ matrix.component.entry }}" \ -profile docker,mount_temp,no_publish \ - -c workflows/utils/labels_ci.config + -c src/workflows/utils/labels_ci.config diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 536e8743ed6..758a4d1127e 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -1,24 +1,136 @@ -name: main build +name: Build concurrency: - group: main_build + group: ${{ github.workflow }}-${{ github.event.inputs.deploy_branch && format('{0}_build', github.ref_name) || github.event.inputs.deploy_branch }} cancel-in-progress: true on: + workflow_dispatch: + inputs: + push_containers: + type: boolean + required: false + default: false + description: Build docker images and push them to the registry + version: + type: string + required: false + description: | + Version to tag the build components with (e.i functionality.version). + Defaults to name of the branch that triggered the workflow, suffixed by "_build". + target_tag: + type: string + required: false + default: main_build + description: | + Version tag of containers to use. Is `main_build` by default. + Can be used in combination with 'push_containers' to re-use existing docker images + or set the tag for new builds. + deploy_to_viash_hub: + type: boolean + required: false + default: false + description: Also build packages and docker images for viash-hub.com and push them. + + # when used as a subworkflow + workflow_call: + inputs: + push_containers: + type: boolean + required: false + default: false + description: push the containers to the registry + version: + type: string + required: false + description: | + Version to tag the build components with (e.i functionality.version). + Defaults to name of the branch that triggered the workflow, suffixed by "_build". + target_tag: + type: string + required: false + default: main_build + description: Version tag of existing containers to use. Is `main_build` by default. + deploy_branch: + type: string + required: false + description: | + Branch to deploy the build to. Defaults to name of the branch + that triggered the workflow, suffixed by "_build". + deploy_to_viash_hub: + type: boolean + required: false + default: false + description: Also build packages and docker images for viash-hub.com and push them. + outputs: + component_matrix: + description: "A JSON object that can be used to populate a github actions matrix for component jobs." + value: ${{ jobs.build_and_deploy_target_folder.outputs.component_matrix }} + workflow_matrix: + description: "A JSON object that can be used to populate a github actions matrix for workflow jobs." + value: ${{ jobs.build_and_deploy_target_folder.outputs.workflow_matrix}} + secrets: + VIASHHUB_USER: + required: true + VIASHHUB_PAT: + required: true + GTHB_USER: + required: true + GTHB_PAT: + required: true push: branches: [ 'main' ] + jobs: # phase 1 - list: + build_and_deploy_target_folder: + name: "Build and push target folder" runs-on: ubuntu-latest outputs: - component_matrix: ${{ steps.set_matrix.outputs.matrix }} - cache_key: ${{ steps.cache.outputs.cache_key }} + component_matrix: ${{ steps.set_matrix.outputs.components }} + workflow_matrix: ${{ steps.set_matrix.outputs.workflows }} + + env: + DEPLOY_BRANCH: ${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }} steps: + - name: Keep symlinks as-is + run: | + git config --global core.symlinks true + + - uses: actions/checkout@v4 + if: ${{ inputs.deploy_to_viash_hub == 'true' }} + with: + fetch-depth: 0 + + - name: Push ref to Viash-hub + if: ${{ inputs.deploy_to_viash_hub == 'true' }} + run: | + git remote add viash-hub https://x-access-token:${{ secrets.VIASHHUB_PAT }}@viash-hub.com/openpipelines-bio/openpipeline.git + git push -f -u viash-hub ${{ github.ref_name }} + + - name: Branch to checkout (use existing target branch if it exists) + id: get_checkout_branch + run: | + if ! git ls-remote --heads --exit-code https://github.com/openpipelines-bio/openpipeline.git "$DEPLOY_BRANCH" > /dev/null; then + echo "Remote branch does not exist, fetching current branch and building on top of it" + echo "checkout_branch=${{ github.ref_name }}" >> "$GITHUB_OUTPUT" + else + echo "Remote branch exists, checking out existing branch" + echo "checkout_branch=$DEPLOY_BRANCH" >> "$GITHUB_OUTPUT" + fi + - uses: actions/checkout@v4 + with: + ref: ${{ steps.get_checkout_branch.outputs.checkout_branch }} + fetch-depth: 0 + - name: Fetch changes from ${{github.ref_name}} + run: | + git fetch origin ${{github.ref_name}} + git checkout -f --no-overlay origin/${{github.ref_name}} -- '.' + - uses: viash-io/viash-actions/setup@v4 - name: Remove target folder from .gitignore @@ -28,43 +140,62 @@ jobs: - uses: viash-io/viash-actions/ns-build@v4 with: - config_mod: .functionality.version := 'main_build' + config_mod: | + .functionality.version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" + .platforms[.type == 'docker'].target_tag := '${{ github.event_name == 'push' && 'main_build' || inputs.target_tag }}' parallel: true - + query: ^(?!workflows) + + - uses: viash-io/viash-actions/ns-build@v4 + with: + config_mod: .functionality.version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" + parallel: true + query: ^workflows + - name: Build nextflow schemas uses: viash-io/viash-actions/pro/build-nextflow-schemas@v4 with: - workflows: workflows components: src + workflows: src viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' - name: Build parameter files uses: viash-io/viash-actions/pro/build-nextflow-params@v4 with: - workflows: workflows + workflows: src components: src viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' - name: Deploy to target branch - uses: peaceiris/actions-gh-pages@v3 + uses: stefanzweifel/git-auto-commit-action@v5 with: - github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: . - publish_branch: main_build - exclude_assets: '' - - - id: ns_list + create_branch: true + commit_message: "deploy: ${{github.sha}}" + skip_dirty_check: true + branch: ${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }} + - name: "List components" + id: ns_list uses: viash-io/viash-actions/ns-list@v4 with: platform: docker src: src format: json + query_namespace: ^(?!workflows) - - id: set_matrix + - name: "List workflows" + id: ns_list_workflows + uses: viash-io/viash-actions/ns-list@v4 + with: + src: src + format: json + query_namespace: ^workflows + + - name: "Parse JSON output from 'viash ns list' as input for matrix." + id: set_matrix run: | - echo "matrix=$(jq -c '[ .[] | + echo "components=$(jq -c '[ .[] | { "name": (.functionality.namespace + "/" + .functionality.name), "config": .info.config, @@ -72,16 +203,82 @@ jobs: } ]' ${{ steps.ns_list.outputs.output_file }} )" >> $GITHUB_OUTPUT + echo "workflows=$(jq -c '[ .[] | . as $config | (.functionality.test_resources // [])[] | select(.type == "nextflow_script", .entrypoint) | + { + "name": ($config.functionality.namespace + "/" + $config.functionality.name), + "main_script": (($config.info.config | capture("^(?.*\/)").dir) + "/" + .path), + "entry": .entrypoint, + "config": $config.info.config + } + ] | unique' ${{ steps.ns_list_workflows.outputs.output_file }} )" >> $GITHUB_OUTPUT + + - uses: actions/checkout@v4 + if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} + with: + ref: ${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }} + fetch-depth: 0 + clean: true + + - name: Set origin to viash-hub and commit on top of it. + if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} + # This is needed because git-auto-commit-action uses origin by default + run: | + git remote add viash-hub https://x-access-token:${{ secrets.VIASHHUB_PAT }}@viash-hub.com/openpipelines-bio/openpipeline.git + if git ls-remote --heads --exit-code https://viash-hub.com/openpipelines-bio/openpipeline.git ${{ github.ref_name }}_build > /dev/null; then + git fetch viash-hub ${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }} + git reset --hard viash-hub/${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }} + fi + git checkout -f --no-overlay origin/${{github.ref_name}} -- '.' + git remote set-url origin https://x-access-token:${{ secrets.VIASHHUB_PAT }}@viash-hub.com/openpipelines-bio/openpipeline.git + git remote rm viash-hub + + - name: Remove target folder from .gitignore + run: | + # allow publishing the target folder + sed -i '/^\/target\/$/d' .gitignore + + - uses: viash-io/viash-actions/ns-build@v4 + if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} + with: + config_mod: | + .functionality.version := " ${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }}" + .platforms[.type == 'docker'].target_tag := '${{ github.event_name == 'push' && 'main_build' || inputs.target_tag }}' + .platforms[.type == 'docker'].target_organization := 'openpipelines-bio/openpipeline' + .platforms[.type == 'docker'].target_registry := 'viash-hub.com:5050' + .platforms[.type == 'docker'].target_image_source := 'https://viash-hub.com/openpipelines-bio/openpipeline' + parallel: true + query: ^(?!workflows) + + - uses: viash-io/viash-actions/ns-build@v4 + if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} + with: + config_mod: | + .functionality.version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" + parallel: true + query: ^workflows + + - name: Deploy to target branch + if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} + uses: stefanzweifel/git-auto-commit-action@v5 + with: + create_branch: true + commit_message: "deploy: ${{github.sha}}" + skip_dirty_check: true + branch: ${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }} + skip_checkout: true + # phase 2 - build: - needs: list + build_and_deploy_docker_containers: + name: "Build and Deploy Docker Images" + needs: build_and_deploy_target_folder + if: ${{github.event_name == 'push' || inputs.push_containers }} runs-on: ubuntu-latest strategy: fail-fast: false matrix: - component: ${{ fromJson(needs.list.outputs.component_matrix) }} + component: ${{ fromJson(needs.build_and_deploy_target_folder.outputs.component_matrix) }} steps: # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' @@ -94,7 +291,9 @@ jobs: - name: Build container uses: viash-io/viash-actions/ns-build@v4 with: - config_mod: .functionality.version := 'main_build' + config_mod: | + .functionality.version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" + .platforms[.type == 'docker'].target_tag := '${{ github.event_name == 'push' && 'main_build' || inputs.target_tag }}' platform: docker src: ${{ matrix.component.dir }} setup: build @@ -109,7 +308,40 @@ jobs: - name: Push container uses: viash-io/viash-actions/ns-build@v4 with: - config_mod: .functionality.version := 'main_build' + config_mod: .functionality.version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" + platform: docker + src: ${{ matrix.component.dir }} + setup: push + + - name: Login to Viash-Hub container registry + if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} + uses: docker/login-action@v3 + with: + registry: viash-hub.com:5050 + username: ${{ secrets.VIASHHUB_USER }} + password: ${{ secrets.VIASHHUB_PAT }} + + - name: Update Docker settings + if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} + run: | + sudo sed -i 's/ }/, \"max-concurrent-uploads\": 2 }/' /etc/docker/daemon.json + sudo systemctl restart docker + + - name: "Re-tag containers for viash-hub" + if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} + run: | + viash ns exec -s ${{ matrix.component.dir }} --apply_platform -p docker \ + 'docker tag ghcr.io/openpipelines-bio/{namespace}_{functionality-name}:${{ github.event_name == 'push' && 'main_build' || inputs.target_tag }} viash-hub.com:5050/openpipelines-bio/openpipeline/{namespace}_{functionality-name}:${{ github.ref_name }}_build' + + - name: Push container to Viash-Hub + if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} + uses: viash-io/viash-actions/ns-build@v4 + with: + config_mod: | + .functionality.version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" + .platforms[.type == 'docker'].target_registry := 'viash-hub.com:5050' + .platforms[.type == 'docker'].target_organization := 'openpipelines-bio/openpipeline' + .platforms[.type == 'docker'].target_image_source := 'https://viash-hub.com/openpipelines-bio/openpipeline' platform: docker src: ${{ matrix.component.dir }} - setup: push \ No newline at end of file + setup: push diff --git a/.github/workflows/release-build-viash-hub.yml b/.github/workflows/release-build-viash-hub.yml index 382909746c9..2c44040d73b 100644 --- a/.github/workflows/release-build-viash-hub.yml +++ b/.github/workflows/release-build-viash-hub.yml @@ -49,11 +49,13 @@ jobs: .platforms[.type == 'docker'].target_organization := 'openpipelines-bio/openpipeline' .platforms[.type == 'docker'].target_image_source := 'https://viash-hub.com/openpipelines-bio/openpipeline' parallel: true + query_namespace: ^(?!workflows) + - name: Build nextflow schemas uses: viash-io/viash-actions/pro/build-nextflow-schemas@v4 with: - workflows: workflows + workflows: src components: src viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' @@ -61,7 +63,7 @@ jobs: - name: Build parameter files uses: viash-io/viash-actions/pro/build-nextflow-params@v4 with: - workflows: workflows + workflows: src components: src viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' @@ -81,14 +83,14 @@ jobs: uses: viash-io/viash-actions/ns-list@v4 with: platform: docker - src: src format: json + query_namespace: ^(?!workflows) - id: ns_list_workflows uses: viash-io/viash-actions/ns-list@v4 with: - src: workflows format: json + query_namespace: ^workflows - id: set_matrix run: | @@ -181,7 +183,7 @@ jobs: - uses: viash-io/viash-actions/setup@v4 - - uses: nf-core/setup-nextflow@v1.3.0 + - uses: nf-core/setup-nextflow@v1.5.0 # build target dir # use containers from release branch, hopefully these are available @@ -198,7 +200,7 @@ jobs: # use cache - name: Cache resources data - uses: actions/cache@v3 + uses: actions/cache@v4 timeout-minutes: 5 with: path: resources_test @@ -234,7 +236,7 @@ jobs: -main-script "${{ matrix.component.main_script }}" \ -entry ${{ matrix.component.entry }} \ -profile docker,mount_temp,no_publish \ - -c workflows/utils/labels_ci.config + -c src/workflows/utils/labels_ci.config ###################################3 # phase 4 @@ -259,7 +261,7 @@ jobs: # use cache - name: Cache resources data id: restore_cache - uses: actions/cache/restore@v3 + uses: actions/cache/restore@v4 env: SEGMENT_DOWNLOAD_TIMEOUT_MINS: 5 with: diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index a92d51c990f..3fbf7f1c1b4 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -40,11 +40,12 @@ jobs: with: config_mod: ".functionality.version := '${{ github.event.inputs.version_tag }}'" parallel: true + query_namespace: ^(?!workflows) - name: Build nextflow schemas uses: viash-io/viash-actions/pro/build-nextflow-schemas@v4 with: - workflows: workflows + workflows: src components: src viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' @@ -52,7 +53,7 @@ jobs: - name: Build parameter files uses: viash-io/viash-actions/pro/build-nextflow-params@v4 with: - workflows: workflows + workflows: src components: src viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' @@ -71,14 +72,14 @@ jobs: uses: viash-io/viash-actions/ns-list@v4 with: platform: docker - src: src format: json + query_namespace: ^(?!workflows) - id: ns_list_workflows uses: viash-io/viash-actions/ns-list@v4 with: - src: workflows format: json + query_namespace: ^workflows - id: set_matrix run: | @@ -163,7 +164,7 @@ jobs: - uses: viash-io/viash-actions/setup@v4 - - uses: nf-core/setup-nextflow@v1.3.0 + - uses: nf-core/setup-nextflow@v1.5.0 # build target dir # use containers from release branch, hopefully these are available @@ -176,7 +177,7 @@ jobs: # use cache - name: Cache resources data - uses: actions/cache@v3 + uses: actions/cache@v4 timeout-minutes: 5 with: path: resources_test @@ -212,7 +213,7 @@ jobs: -main-script "${{ matrix.component.main_script }}" \ -entry ${{ matrix.component.entry }} \ -profile docker,mount_temp,no_publish \ - -c workflows/utils/labels_ci.config + -c src/workflows/utils/labels_ci.config ###################################3 # phase 4 @@ -237,7 +238,7 @@ jobs: # use cache - name: Cache resources data id: restore_cache - uses: actions/cache/restore@v3 + uses: actions/cache/restore@v4 env: SEGMENT_DOWNLOAD_TIMEOUT_MINS: 5 with: diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 369a51db013..05033a85072 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -56,7 +56,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v39 + uses: tj-actions/changed-files@v42 with: separator: ";" diff_relative: true @@ -66,6 +66,7 @@ jobs: with: platform: docker format: json + query_namespace: ^(?!workflows) - id: ns_list_filtered uses: viash-io/viash-actions/project/detect-changed-components@v4 @@ -104,7 +105,7 @@ jobs: # use cache - name: Cache resources data id: restore_cache - uses: actions/cache/restore@v3 + uses: actions/cache/restore@v4 env: SEGMENT_DOWNLOAD_TIMEOUT_MINS: 5 with: From 72c71777ec96f0812f52a03b52ceaefaff28e0c6 Mon Sep 17 00:00:00 2001 From: DriesSchaumont Date: Thu, 25 Jan 2024 10:16:04 +0000 Subject: [PATCH 3/4] deploy: 827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f --- target/docker/annotate/popv/.config.vsh.yaml | 4 +- target/docker/annotate/popv/popv | 4 +- target/docker/cluster/leiden/.config.vsh.yaml | 4 +- target/docker/cluster/leiden/leiden | 4 +- .../compress_h5mu/.config.vsh.yaml | 4 +- .../compression/compress_h5mu/compress_h5mu | 4 +- .../compression/tar_extract/.config.vsh.yaml | 4 +- .../compression/tar_extract/tar_extract | 4 +- .../from_10xh5_to_h5mu/.config.vsh.yaml | 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.../mapping/cellranger_multi/cellranger_multi | 4 +- .../mapping/htseq_count/.config.vsh.yaml | 4 +- target/docker/mapping/htseq_count/htseq_count | 4 +- .../htseq_count_to_h5mu/.config.vsh.yaml | 4 +- .../htseq_count_to_h5mu/htseq_count_to_h5mu | 4 +- .../mapping/multi_star/.config.vsh.yaml | 4 +- target/docker/mapping/multi_star/multi_star | 4 +- .../multi_star_to_h5mu/.config.vsh.yaml | 4 +- .../multi_star_to_h5mu/multi_star_to_h5mu | 4 +- .../mapping/samtools_sort/.config.vsh.yaml | 4 +- .../mapping/samtools_sort/samtools_sort | 4 +- .../mapping/star_align/.config.vsh.yaml | 4 +- target/docker/mapping/star_align/star_align | 4 +- .../mapping/star_align_v273a/.config.vsh.yaml | 4 +- .../mapping/star_align_v273a/star_align_v273a | 4 +- .../star_build_reference/.config.vsh.yaml | 4 +- .../star_build_reference/star_build_reference | 4 +- .../docker/metadata/add_id/.config.vsh.yaml | 4 +- target/docker/metadata/add_id/add_id | 4 +- .../grep_annotation_column/.config.vsh.yaml | 4 +- .../grep_annotation_column | 4 +- .../docker/metadata/join_csv/.config.vsh.yaml | 4 +- target/docker/metadata/join_csv/join_csv | 4 +- .../metadata/join_uns_to_obs/.config.vsh.yaml | 4 +- .../metadata/join_uns_to_obs/join_uns_to_obs | 4 +- .../move_obsm_to_obs/.config.vsh.yaml | 4 +- .../move_obsm_to_obs/move_obsm_to_obs | 4 +- .../docker/neighbors/bbknn/.config.vsh.yaml | 4 +- target/docker/neighbors/bbknn/bbknn | 4 +- .../neighbors/find_neighbors/.config.vsh.yaml | 4 +- .../neighbors/find_neighbors/find_neighbors | 4 +- .../filter_10xh5/.config.vsh.yaml | 4 +- .../process_10xh5/filter_10xh5/filter_10xh5 | 4 +- .../qc/calculate_qc_metrics/.config.vsh.yaml | 4 +- .../calculate_qc_metrics/calculate_qc_metrics | 4 +- target/docker/qc/fastqc/.config.vsh.yaml | 4 +- target/docker/qc/fastqc/fastqc | 4 +- target/docker/qc/multiqc/.config.vsh.yaml | 4 +- target/docker/qc/multiqc/multiqc | 4 +- .../query/cellxgene_census/.config.vsh.yaml | 4 +- .../query/cellxgene_census/cellxgene_census | 4 +- .../build_bdrhap_reference/.config.vsh.yaml | 4 +- .../build_bdrhap_reference | 4 +- .../.config.vsh.yaml | 4 +- .../build_cellranger_reference | 4 +- .../reference/make_reference/.config.vsh.yaml | 4 +- .../reference/make_reference/make_reference | 4 +- target/docker/report/mermaid/.config.vsh.yaml | 4 +- target/docker/report/mermaid/mermaid | 4 +- .../docker/transfer/publish/.config.vsh.yaml | 4 +- target/docker/transfer/publish/publish | 4 +- target/docker/transform/clr/.config.vsh.yaml | 4 +- target/docker/transform/clr/clr | 4 +- .../transform/delete_layer/.config.vsh.yaml | 4 +- .../transform/delete_layer/delete_layer | 4 +- .../docker/transform/log1p/.config.vsh.yaml | 4 +- target/docker/transform/log1p/log1p | 4 +- .../normalize_total/.config.vsh.yaml | 4 +- .../transform/normalize_total/normalize_total | 4 +- .../transform/regress_out/.config.vsh.yaml | 4 +- .../docker/transform/regress_out/regress_out | 4 +- .../docker/transform/scale/.config.vsh.yaml | 4 +- target/docker/transform/scale/scale | 4 +- .../docker/velocity/scvelo/.config.vsh.yaml | 4 +- target/docker/velocity/scvelo/scvelo | 4 +- .../docker/velocity/velocyto/.config.vsh.yaml | 4 +- target/docker/velocity/velocyto/velocyto | 4 +- .../compress_h5mu/.config.vsh.yaml | 4 +- .../compression/tar_extract/.config.vsh.yaml | 4 +- .../native/dataflow/concat/.config.vsh.yaml | 4 +- target/native/dataflow/concat/concat | 37 +++++++++-------- target/native/dataflow/merge/.config.vsh.yaml | 4 +- .../split_modalities/.config.vsh.yaml | 4 +- .../sync_test_resources/.config.vsh.yaml | 4 +- .../integrate/scarches/.config.vsh.yaml | 4 +- .../native/integrate/totalvi/.config.vsh.yaml | 4 +- .../labels_transfer/knn/.config.vsh.yaml | 4 +- .../labels_transfer/xgboost/.config.vsh.yaml | 4 +- .../native/metadata/add_id/.config.vsh.yaml | 4 +- .../grep_annotation_column/.config.vsh.yaml | 4 +- .../native/transform/scale/.config.vsh.yaml | 4 +- .../native/velocity/scvelo/.config.vsh.yaml | 4 +- .../native/velocity/velocyto/.config.vsh.yaml | 4 +- .../nextflow/annotate/popv/.config.vsh.yaml | 4 +- target/nextflow/annotate/popv/main.nf | 4 +- .../nextflow/cluster/leiden/.config.vsh.yaml | 4 +- target/nextflow/cluster/leiden/main.nf | 4 +- .../compress_h5mu/.config.vsh.yaml | 4 +- .../compression/compress_h5mu/main.nf | 4 +- .../from_10xh5_to_h5mu/.config.vsh.yaml | 4 +- .../convert/from_10xh5_to_h5mu/main.nf | 4 +- .../from_10xmtx_to_h5mu/.config.vsh.yaml | 4 +- .../convert/from_10xmtx_to_h5mu/main.nf | 4 +- .../.config.vsh.yaml | 4 +- .../main.nf | 4 +- .../from_bdrhap_to_h5mu/.config.vsh.yaml | 4 +- .../convert/from_bdrhap_to_h5mu/main.nf | 4 +- .../.config.vsh.yaml | 4 +- .../from_cellranger_multi_to_h5mu/main.nf | 4 +- .../from_h5ad_to_h5mu/.config.vsh.yaml | 4 +- .../convert/from_h5ad_to_h5mu/main.nf | 4 +- .../from_h5mu_to_h5ad/.config.vsh.yaml | 4 +- .../convert/from_h5mu_to_h5ad/main.nf | 4 +- .../convert/velocyto_to_h5mu/.config.vsh.yaml | 4 +- .../nextflow/convert/velocyto_to_h5mu/main.nf | 4 +- .../.config.vsh.yaml | 4 +- .../cellbender_remove_background/main.nf | 4 +- .../.config.vsh.yaml | 4 +- .../cellbender_remove_background_v0_2/main.nf | 4 +- .../nextflow/dataflow/concat/.config.vsh.yaml | 4 +- target/nextflow/dataflow/concat/main.nf | 41 ++++++++++--------- .../nextflow/dataflow/merge/.config.vsh.yaml | 4 +- target/nextflow/dataflow/merge/main.nf | 4 +- .../split_modalities/.config.vsh.yaml | 4 +- .../dataflow/split_modalities/main.nf | 4 +- .../nextflow/demux/bcl2fastq/.config.vsh.yaml | 4 +- target/nextflow/demux/bcl2fastq/main.nf | 4 +- .../demux/bcl_convert/.config.vsh.yaml | 4 +- target/nextflow/demux/bcl_convert/main.nf | 4 +- .../demux/cellranger_mkfastq/.config.vsh.yaml | 4 +- .../nextflow/demux/cellranger_mkfastq/main.nf | 4 +- target/nextflow/dimred/pca/.config.vsh.yaml | 4 +- target/nextflow/dimred/pca/main.nf | 4 +- target/nextflow/dimred/umap/.config.vsh.yaml | 4 +- target/nextflow/dimred/umap/main.nf | 4 +- .../download/download_file/.config.vsh.yaml | 4 +- .../nextflow/download/download_file/main.nf | 4 +- .../sync_test_resources/.config.vsh.yaml | 4 +- .../download/sync_test_resources/main.nf | 4 +- .../files/make_params/.config.vsh.yaml | 4 +- target/nextflow/files/make_params/main.nf | 4 +- .../filter/delimit_fraction/.config.vsh.yaml | 4 +- .../nextflow/filter/delimit_fraction/main.nf | 4 +- .../filter/do_filter/.config.vsh.yaml | 4 +- target/nextflow/filter/do_filter/main.nf | 4 +- .../filter_with_counts/.config.vsh.yaml | 4 +- .../filter/filter_with_counts/main.nf | 4 +- .../filter/filter_with_hvg/.config.vsh.yaml | 4 +- .../nextflow/filter/filter_with_hvg/main.nf | 4 +- .../filter_with_scrublet/.config.vsh.yaml | 4 +- .../filter/filter_with_scrublet/main.nf | 4 +- .../filter/remove_modality/.config.vsh.yaml | 4 +- .../nextflow/filter/remove_modality/main.nf | 4 +- .../filter/subset_h5mu/.config.vsh.yaml | 4 +- target/nextflow/filter/subset_h5mu/main.nf | 4 +- .../integrate/harmonypy/.config.vsh.yaml | 4 +- target/nextflow/integrate/harmonypy/main.nf | 4 +- .../integrate/scanorama/.config.vsh.yaml | 4 +- target/nextflow/integrate/scanorama/main.nf | 4 +- .../integrate/scarches/.config.vsh.yaml | 4 +- target/nextflow/integrate/scarches/main.nf | 4 +- .../nextflow/integrate/scvi/.config.vsh.yaml | 4 +- target/nextflow/integrate/scvi/main.nf | 4 +- .../integrate/totalvi/.config.vsh.yaml | 4 +- target/nextflow/integrate/totalvi/main.nf | 4 +- .../interpret/lianapy/.config.vsh.yaml | 4 +- target/nextflow/interpret/lianapy/main.nf | 4 +- .../labels_transfer/knn/.config.vsh.yaml | 4 +- target/nextflow/labels_transfer/knn/main.nf | 4 +- .../labels_transfer/xgboost/.config.vsh.yaml | 4 +- .../nextflow/labels_transfer/xgboost/main.nf | 4 +- .../mapping/bd_rhapsody/.config.vsh.yaml | 4 +- target/nextflow/mapping/bd_rhapsody/main.nf | 4 +- .../mapping/cellranger_count/.config.vsh.yaml | 4 +- .../nextflow/mapping/cellranger_count/main.nf | 4 +- .../cellranger_count_split/.config.vsh.yaml | 4 +- .../mapping/cellranger_count_split/main.nf | 4 +- .../mapping/cellranger_multi/.config.vsh.yaml | 4 +- .../nextflow/mapping/cellranger_multi/main.nf | 4 +- .../mapping/htseq_count/.config.vsh.yaml | 4 +- target/nextflow/mapping/htseq_count/main.nf | 4 +- .../htseq_count_to_h5mu/.config.vsh.yaml | 4 +- .../mapping/htseq_count_to_h5mu/main.nf | 4 +- .../mapping/multi_star/.config.vsh.yaml | 4 +- target/nextflow/mapping/multi_star/main.nf | 4 +- .../multi_star_to_h5mu/.config.vsh.yaml | 4 +- .../mapping/multi_star_to_h5mu/main.nf | 4 +- .../mapping/samtools_sort/.config.vsh.yaml | 4 +- target/nextflow/mapping/samtools_sort/main.nf | 4 +- .../mapping/star_align/.config.vsh.yaml | 4 +- target/nextflow/mapping/star_align/main.nf | 4 +- .../mapping/star_align_v273a/.config.vsh.yaml | 4 +- .../nextflow/mapping/star_align_v273a/main.nf | 4 +- .../star_build_reference/.config.vsh.yaml | 4 +- .../mapping/star_build_reference/main.nf | 4 +- .../nextflow/metadata/add_id/.config.vsh.yaml | 4 +- target/nextflow/metadata/add_id/main.nf | 4 +- .../grep_annotation_column/.config.vsh.yaml | 4 +- .../metadata/grep_annotation_column/main.nf | 4 +- .../metadata/join_csv/.config.vsh.yaml | 4 +- target/nextflow/metadata/join_csv/main.nf | 4 +- .../metadata/join_uns_to_obs/.config.vsh.yaml | 4 +- .../nextflow/metadata/join_uns_to_obs/main.nf | 4 +- .../move_obsm_to_obs/.config.vsh.yaml | 4 +- .../metadata/move_obsm_to_obs/main.nf | 4 +- .../nextflow/neighbors/bbknn/.config.vsh.yaml | 4 +- target/nextflow/neighbors/bbknn/main.nf | 4 +- .../neighbors/find_neighbors/.config.vsh.yaml | 4 +- .../nextflow/neighbors/find_neighbors/main.nf | 4 +- .../filter_10xh5/.config.vsh.yaml | 4 +- .../process_10xh5/filter_10xh5/main.nf | 4 +- .../qc/calculate_qc_metrics/.config.vsh.yaml | 4 +- .../nextflow/qc/calculate_qc_metrics/main.nf | 4 +- target/nextflow/qc/fastqc/.config.vsh.yaml | 4 +- target/nextflow/qc/fastqc/main.nf | 4 +- target/nextflow/qc/multiqc/.config.vsh.yaml | 4 +- target/nextflow/qc/multiqc/main.nf | 4 +- .../query/cellxgene_census/.config.vsh.yaml | 4 +- .../nextflow/query/cellxgene_census/main.nf | 4 +- .../build_bdrhap_reference/.config.vsh.yaml | 4 +- .../reference/build_bdrhap_reference/main.nf | 4 +- .../.config.vsh.yaml | 4 +- .../build_cellranger_reference/main.nf | 4 +- .../reference/make_reference/.config.vsh.yaml | 4 +- .../nextflow/reference/make_reference/main.nf | 4 +- .../nextflow/report/mermaid/.config.vsh.yaml | 4 +- target/nextflow/report/mermaid/main.nf | 4 +- .../transfer/publish/.config.vsh.yaml | 4 +- target/nextflow/transfer/publish/main.nf | 4 +- .../nextflow/transform/clr/.config.vsh.yaml | 4 +- target/nextflow/transform/clr/main.nf | 4 +- .../transform/delete_layer/.config.vsh.yaml | 4 +- .../nextflow/transform/delete_layer/main.nf | 4 +- .../nextflow/transform/log1p/.config.vsh.yaml | 4 +- target/nextflow/transform/log1p/main.nf | 4 +- .../normalize_total/.config.vsh.yaml | 4 +- .../transform/normalize_total/main.nf | 4 +- .../transform/regress_out/.config.vsh.yaml | 4 +- target/nextflow/transform/regress_out/main.nf | 4 +- .../nextflow/transform/scale/.config.vsh.yaml | 4 +- target/nextflow/transform/scale/main.nf | 4 +- .../nextflow/velocity/scvelo/.config.vsh.yaml | 4 +- target/nextflow/velocity/scvelo/main.nf | 4 +- .../velocity/velocyto/.config.vsh.yaml | 4 +- target/nextflow/velocity/velocyto/main.nf | 4 +- 326 files changed, 707 insertions(+), 704 deletions(-) diff --git a/target/docker/annotate/popv/.config.vsh.yaml b/target/docker/annotate/popv/.config.vsh.yaml index 8f4e81a8870..d595e6e7d5c 100644 --- a/target/docker/annotate/popv/.config.vsh.yaml +++ b/target/docker/annotate/popv/.config.vsh.yaml @@ -341,6 +341,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/annotate/popv" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/annotate/popv/popv" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/annotate/popv/popv b/target/docker/annotate/popv/popv index 2addebbf457..5d1d6c02249 100755 --- a/target/docker/annotate/popv/popv +++ b/target/docker/annotate/popv/popv @@ -488,9 +488,9 @@ RUN cd /opt && git clone --depth 1 https://github.com/YosefLab/PopV.git && \ LABEL org.opencontainers.image.authors="Matthias Beyens, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component annotate popv" -LABEL org.opencontainers.image.created="2024-01-25T09:34:40Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:59Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/cluster/leiden/.config.vsh.yaml b/target/docker/cluster/leiden/.config.vsh.yaml index 58ba393a431..b108de8f22e 100644 --- a/target/docker/cluster/leiden/.config.vsh.yaml +++ b/target/docker/cluster/leiden/.config.vsh.yaml @@ -214,6 +214,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/cluster/leiden" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/cluster/leiden/leiden" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/cluster/leiden/leiden b/target/docker/cluster/leiden/leiden index 91c9e0d14b3..d8b5d51ec91 100755 --- a/target/docker/cluster/leiden/leiden +++ b/target/docker/cluster/leiden/leiden @@ -445,9 +445,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer" LABEL org.opencontainers.image.description="Companion container for running component cluster leiden" -LABEL org.opencontainers.image.created="2024-01-25T09:34:36Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:59Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/compression/compress_h5mu/.config.vsh.yaml b/target/docker/compression/compress_h5mu/.config.vsh.yaml index 09a7c5b5924..82c3f368ea4 100644 --- a/target/docker/compression/compress_h5mu/.config.vsh.yaml +++ b/target/docker/compression/compress_h5mu/.config.vsh.yaml @@ -162,6 +162,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/compress_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/compress_h5mu/compress_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/compression/compress_h5mu/compress_h5mu b/target/docker/compression/compress_h5mu/compress_h5mu index 8b12d4c5b86..e4f20ce9654 100755 --- a/target/docker/compression/compress_h5mu/compress_h5mu +++ b/target/docker/compression/compress_h5mu/compress_h5mu @@ -408,9 +408,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component compression compress_h5mu" -LABEL org.opencontainers.image.created="2024-01-25T09:34:36Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:59Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/compression/tar_extract/.config.vsh.yaml b/target/docker/compression/tar_extract/.config.vsh.yaml index 97d51d01bb6..e6ea892a4ca 100644 --- a/target/docker/compression/tar_extract/.config.vsh.yaml +++ b/target/docker/compression/tar_extract/.config.vsh.yaml @@ -101,6 +101,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/tar_extract" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/tar_extract/tar_extract" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/compression/tar_extract/tar_extract b/target/docker/compression/tar_extract/tar_extract index b1293f62f00..6ae8af87aee 100755 --- a/target/docker/compression/tar_extract/tar_extract +++ b/target/docker/compression/tar_extract/tar_extract @@ -406,9 +406,9 @@ ENTRYPOINT [] RUN : LABEL org.opencontainers.image.description="Companion container for running component compression tar_extract" -LABEL org.opencontainers.image.created="2024-01-25T09:34:36Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:59Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/convert/from_10xh5_to_h5mu/.config.vsh.yaml b/target/docker/convert/from_10xh5_to_h5mu/.config.vsh.yaml index 3b9a8a2014f..253211db1ac 100644 --- a/target/docker/convert/from_10xh5_to_h5mu/.config.vsh.yaml +++ b/target/docker/convert/from_10xh5_to_h5mu/.config.vsh.yaml @@ -267,6 +267,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_10xh5_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu b/target/docker/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu index 0b206ce9bd3..bd646a2b95b 100755 --- a/target/docker/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu +++ b/target/docker/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu @@ -430,9 +430,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component convert from_10xh5_to_h5mu" -LABEL org.opencontainers.image.created="2024-01-25T09:34:34Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:56Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/convert/from_10xmtx_to_h5mu/.config.vsh.yaml b/target/docker/convert/from_10xmtx_to_h5mu/.config.vsh.yaml index 984e3b8fed2..9828a537c5f 100644 --- a/target/docker/convert/from_10xmtx_to_h5mu/.config.vsh.yaml +++ b/target/docker/convert/from_10xmtx_to_h5mu/.config.vsh.yaml @@ -161,6 +161,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_10xmtx_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu b/target/docker/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu index 78dfbe37df7..12d25de3753 100755 --- a/target/docker/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu +++ b/target/docker/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu @@ -408,9 +408,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component convert from_10xmtx_to_h5mu" -LABEL org.opencontainers.image.created="2024-01-25T09:34:39Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:55Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml b/target/docker/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml index 5d6708e616e..7e86c69dedb 100644 --- a/target/docker/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml +++ b/target/docker/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml @@ -154,6 +154,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_bd_to_10x_molecular_barcode_tags" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags b/target/docker/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags index 493f5c5c969..00300515cc3 100755 --- a/target/docker/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags +++ b/target/docker/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags @@ -409,9 +409,9 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component convert from_bd_to_10x_molecular_barcode_tags" -LABEL org.opencontainers.image.created="2024-01-25T09:34:34Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:55Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/convert/from_bdrhap_to_h5mu/.config.vsh.yaml b/target/docker/convert/from_bdrhap_to_h5mu/.config.vsh.yaml index 113f8d0f62a..7ecfaba2de3 100644 --- a/target/docker/convert/from_bdrhap_to_h5mu/.config.vsh.yaml +++ b/target/docker/convert/from_bdrhap_to_h5mu/.config.vsh.yaml @@ -176,6 +176,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_bdrhap_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu b/target/docker/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu index e6f95c97523..5914e1e8f9a 100755 --- a/target/docker/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu +++ b/target/docker/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu @@ -414,9 +414,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component convert from_bdrhap_to_h5mu" -LABEL org.opencontainers.image.created="2024-01-25T09:34:34Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:56Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml b/target/docker/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml index c772de00517..2c96fe3a4b8 100644 --- a/target/docker/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml +++ b/target/docker/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml @@ -185,6 +185,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_cellranger_multi_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu b/target/docker/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu index ab10495eea7..4e46b6c0232 100755 --- a/target/docker/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu +++ b/target/docker/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu @@ -427,9 +427,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component convert from_cellranger_multi_to_h5mu" -LABEL org.opencontainers.image.created="2024-01-25T09:34:34Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:56Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/convert/from_h5ad_to_h5mu/.config.vsh.yaml b/target/docker/convert/from_h5ad_to_h5mu/.config.vsh.yaml index 7ca21c65a21..1572fd33043 100644 --- a/target/docker/convert/from_h5ad_to_h5mu/.config.vsh.yaml +++ b/target/docker/convert/from_h5ad_to_h5mu/.config.vsh.yaml @@ -172,6 +172,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_h5ad_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu b/target/docker/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu index f50ef22fe94..cd92d16c44c 100755 --- a/target/docker/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu +++ b/target/docker/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu @@ -412,9 +412,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer" LABEL org.opencontainers.image.description="Companion container for running component convert from_h5ad_to_h5mu" -LABEL org.opencontainers.image.created="2024-01-25T09:34:38Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:55Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/convert/from_h5mu_to_h5ad/.config.vsh.yaml b/target/docker/convert/from_h5mu_to_h5ad/.config.vsh.yaml index 5b0df89feec..e754fa369be 100644 --- a/target/docker/convert/from_h5mu_to_h5ad/.config.vsh.yaml +++ b/target/docker/convert/from_h5mu_to_h5ad/.config.vsh.yaml @@ -177,6 +177,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_h5mu_to_h5ad" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad b/target/docker/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad index 7cfa243b1ec..2ac562b3688 100755 --- a/target/docker/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad +++ b/target/docker/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad @@ -413,9 +413,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_to_h5ad" -LABEL org.opencontainers.image.created="2024-01-25T09:34:38Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:54Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/convert/velocyto_to_h5mu/.config.vsh.yaml b/target/docker/convert/velocyto_to_h5mu/.config.vsh.yaml index d709ed92cba..b84e91db02f 100644 --- a/target/docker/convert/velocyto_to_h5mu/.config.vsh.yaml +++ b/target/docker/convert/velocyto_to_h5mu/.config.vsh.yaml @@ -250,6 +250,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/velocyto_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/velocyto_to_h5mu/velocyto_to_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/convert/velocyto_to_h5mu/velocyto_to_h5mu b/target/docker/convert/velocyto_to_h5mu/velocyto_to_h5mu index aaf78e2a6fd..f379266f1ae 100755 --- a/target/docker/convert/velocyto_to_h5mu/velocyto_to_h5mu +++ b/target/docker/convert/velocyto_to_h5mu/velocyto_to_h5mu @@ -440,9 +440,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt, Angela Oliveira Pisco" LABEL org.opencontainers.image.description="Companion container for running component convert velocyto_to_h5mu" -LABEL org.opencontainers.image.created="2024-01-25T09:34:34Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:58Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/correction/cellbender_remove_background/.config.vsh.yaml b/target/docker/correction/cellbender_remove_background/.config.vsh.yaml index 5f2d345b32e..27e08715776 100644 --- a/target/docker/correction/cellbender_remove_background/.config.vsh.yaml +++ b/target/docker/correction/cellbender_remove_background/.config.vsh.yaml @@ -632,6 +632,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/correction/cellbender_remove_background" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/correction/cellbender_remove_background/cellbender_remove_background" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/correction/cellbender_remove_background/cellbender_remove_background b/target/docker/correction/cellbender_remove_background/cellbender_remove_background index a9b6a82437e..28bee30b0b8 100755 --- a/target/docker/correction/cellbender_remove_background/cellbender_remove_background +++ b/target/docker/correction/cellbender_remove_background/cellbender_remove_background @@ -671,9 +671,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "mudata~=0.2.1" "cellbender~=0.3.0" LABEL org.opencontainers.image.description="Companion container for running component correction cellbender_remove_background" -LABEL org.opencontainers.image.created="2024-01-25T09:34:38Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:58Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/correction/cellbender_remove_background_v0_2/.config.vsh.yaml b/target/docker/correction/cellbender_remove_background_v0_2/.config.vsh.yaml index 217aa1972eb..f797ad4313d 100644 --- a/target/docker/correction/cellbender_remove_background_v0_2/.config.vsh.yaml +++ b/target/docker/correction/cellbender_remove_background_v0_2/.config.vsh.yaml @@ -401,6 +401,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/correction/cellbender_remove_background_v0_2" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/correction/cellbender_remove_background_v0_2/cellbender_remove_background_v0_2" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/correction/cellbender_remove_background_v0_2/cellbender_remove_background_v0_2 b/target/docker/correction/cellbender_remove_background_v0_2/cellbender_remove_background_v0_2 index a41190108c0..3d153df830e 100755 --- a/target/docker/correction/cellbender_remove_background_v0_2/cellbender_remove_background_v0_2 +++ b/target/docker/correction/cellbender_remove_background_v0_2/cellbender_remove_background_v0_2 @@ -537,9 +537,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "mudata~=0.2.3" "anndata~=0.9.1" "muon==0.1.5" "tables==3.8.0" "cellbender==0.2.1" LABEL org.opencontainers.image.description="Companion container for running component correction cellbender_remove_background_v0_2" -LABEL org.opencontainers.image.created="2024-01-25T09:34:38Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:58Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/dataflow/concat/.config.vsh.yaml b/target/docker/dataflow/concat/.config.vsh.yaml index be7b49b3b65..3f0e4975e9e 100644 --- a/target/docker/dataflow/concat/.config.vsh.yaml +++ b/target/docker/dataflow/concat/.config.vsh.yaml @@ -217,6 +217,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/dataflow/concat" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/dataflow/concat/concat" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/dataflow/concat/concat b/target/docker/dataflow/concat/concat index 05a27f05540..d274156f9f5 100755 --- a/target/docker/dataflow/concat/concat +++ b/target/docker/dataflow/concat/concat @@ -437,9 +437,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component dataflow concat" -LABEL org.opencontainers.image.created="2024-01-25T09:34:37Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:58Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER @@ -1132,20 +1132,19 @@ def any_row_contains_duplicate_values(n_processes: int, frame: pd.DataFrame) -> is_duplicated = pool.map(nunique, iter(numpy_array)) return any(is_duplicated) -def concatenate_matrices(n_processes: int, input_ids: tuple[str], matrices: Iterable[pd.DataFrame], align_to: pd.Index | None) \\ +def concatenate_matrices(n_processes: int, matrices: dict[str, pd.DataFrame], align_to: pd.Index | None) \\ -> tuple[dict[str, pd.DataFrame], pd.DataFrame | None, dict[str, pd.core.dtypes.dtypes.Dtype]]: """ Merge matrices by combining columns that have the same name. Columns that contain conflicting values (e.i. the columns have different values), are not merged, but instead moved to a new dataframe. """ - column_names = set(column_name for var in matrices for column_name in var) + column_names = set(column_name for var in matrices.values() for column_name in var) logger.debug('Trying to concatenate columns: %s.', ",".join(column_names)) if not column_names: return {}, pd.DataFrame(index=align_to) conflicts, concatenated_matrix = \\ split_conflicts_and_concatenated_columns(n_processes, - input_ids, matrices, column_names, align_to) @@ -1162,8 +1161,7 @@ def get_first_non_na_value_vector(df): return pd.Series(numpy_arr.ravel()[flat_index], index=df.index, name=df.columns[0]) def split_conflicts_and_concatenated_columns(n_processes: int, - input_ids: tuple[str], - matrices: Iterable[pd.DataFrame], + matrices: dict[str, pd.DataFrame], column_names: Iterable[str], align_to: pd.Index | None = None) -> \\ tuple[dict[str, pd.DataFrame], pd.DataFrame]: @@ -1177,14 +1175,17 @@ def split_conflicts_and_concatenated_columns(n_processes: int, conflicts = {} concatenated_matrix = [] for column_name in column_names: - columns = [var[column_name] for var in matrices if column_name in var] + columns = {input_id: var[column_name] + for input_id, var in matrices.items() + if column_name in var} assert columns, "Some columns should have been found." - concatenated_columns = pd.concat(columns, axis=1, join="outer", sort=False) + concatenated_columns = pd.concat(columns.values(), axis=1, + join="outer", sort=False) if any_row_contains_duplicate_values(n_processes, concatenated_columns): - concatenated_columns.columns = input_ids + concatenated_columns.columns = columns.keys() # Use the sample id as column name if align_to is not None: concatenated_columns = concatenated_columns.reindex(align_to, copy=False) - conflicts[f'conflict_{column_name}'] = concatenated_columns + conflicts[f'conflict_{column_name}'] = concatenated_columns else: unique_values = get_first_non_na_value_vector(concatenated_columns) concatenated_matrix.append(unique_values) @@ -1218,7 +1219,7 @@ def cast_to_writeable_dtype(result: pd.DataFrame) -> pd.DataFrame: result[obj_col] = result[obj_col].where(result[obj_col].isna(), result[obj_col].astype(str)).astype('category') return result -def split_conflicts_modalities(n_processes: int, input_ids: tuple[str], samples: Iterable[anndata.AnnData], output: anndata.AnnData) \\ +def split_conflicts_modalities(n_processes: int, samples: dict[str, anndata.AnnData], output: anndata.AnnData) \\ -> anndata.AnnData: """ Merge .var and .obs matrices of the anndata objects. Columns are merged @@ -1228,10 +1229,10 @@ def split_conflicts_modalities(n_processes: int, input_ids: tuple[str], samples: """ matrices_to_parse = ("var", "obs") for matrix_name in matrices_to_parse: - matrices = [getattr(sample, matrix_name) for sample in samples] + matrices = {sample_id: getattr(sample, matrix_name) for sample_id, sample in samples.items()} output_index = getattr(output, matrix_name).index align_to = output_index if matrix_name == "var" else None - conflicts, concatenated_matrix = concatenate_matrices(n_processes, input_ids, matrices, align_to) + conflicts, concatenated_matrix = concatenate_matrices(n_processes, matrices, align_to) if concatenated_matrix.empty: concatenated_matrix.index = output_index # Write the conflicts to the output @@ -1252,20 +1253,20 @@ def concatenate_modality(n_processes: int, mod: str, input_files: Iterable[str | } other_axis_mode_to_apply = concat_modes.get(other_axis_mode, other_axis_mode) - mod_data = [] - for input_file in input_files: + mod_data = {} + for input_id, input_file in zip(input_ids, input_files): try: - mod_data.append(mu.read_h5ad(input_file, mod=mod)) + mod_data[input_id] = mu.read_h5ad(input_file, mod=mod) except KeyError as e: # Modality does not exist for this sample, skip it if f"Unable to open object '{mod}' doesn't exist" not in str(e): raise e pass - check_observations_unique(mod_data) + check_observations_unique(mod_data.values()) - concatenated_data = anndata.concat(mod_data, join='outer', merge=other_axis_mode_to_apply) + concatenated_data = anndata.concat(mod_data.values(), join='outer', merge=other_axis_mode_to_apply) if other_axis_mode == "move": - concatenated_data = split_conflicts_modalities(n_processes, input_ids, mod_data, concatenated_data) + concatenated_data = split_conflicts_modalities(n_processes, mod_data, concatenated_data) return concatenated_data diff --git a/target/docker/dataflow/merge/.config.vsh.yaml b/target/docker/dataflow/merge/.config.vsh.yaml index 1305cfc0429..65b92df4ab3 100644 --- a/target/docker/dataflow/merge/.config.vsh.yaml +++ b/target/docker/dataflow/merge/.config.vsh.yaml @@ -170,6 +170,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/dataflow/merge" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/dataflow/merge/merge" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/dataflow/merge/merge b/target/docker/dataflow/merge/merge index 5c42f19c0c4..680184215dc 100755 --- a/target/docker/dataflow/merge/merge +++ b/target/docker/dataflow/merge/merge @@ -409,9 +409,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component dataflow merge" -LABEL org.opencontainers.image.created="2024-01-25T09:34:37Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:57Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/dataflow/split_modalities/.config.vsh.yaml b/target/docker/dataflow/split_modalities/.config.vsh.yaml index e29e31a29f9..a32bc5f622b 100644 --- a/target/docker/dataflow/split_modalities/.config.vsh.yaml +++ b/target/docker/dataflow/split_modalities/.config.vsh.yaml @@ -209,6 +209,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/dataflow/split_modalities" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/dataflow/split_modalities/split_modalities" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/dataflow/split_modalities/split_modalities b/target/docker/dataflow/split_modalities/split_modalities index 4b027f76df6..3fa63d3502b 100755 --- a/target/docker/dataflow/split_modalities/split_modalities +++ b/target/docker/dataflow/split_modalities/split_modalities @@ -421,9 +421,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component dataflow split_modalities" -LABEL org.opencontainers.image.created="2024-01-25T09:34:37Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:57Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/demux/bcl2fastq/.config.vsh.yaml b/target/docker/demux/bcl2fastq/.config.vsh.yaml index f27f0e9fe5a..9d0adfe6947 100644 --- a/target/docker/demux/bcl2fastq/.config.vsh.yaml +++ b/target/docker/demux/bcl2fastq/.config.vsh.yaml @@ -164,6 +164,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/demux/bcl2fastq" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/demux/bcl2fastq/bcl2fastq" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/demux/bcl2fastq/bcl2fastq b/target/docker/demux/bcl2fastq/bcl2fastq index 1ed17274201..81fdbb33bc7 100755 --- a/target/docker/demux/bcl2fastq/bcl2fastq +++ b/target/docker/demux/bcl2fastq/bcl2fastq @@ -410,9 +410,9 @@ ENTRYPOINT [] RUN : LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component demux bcl2fastq" -LABEL org.opencontainers.image.created="2024-01-25T09:34:37Z" +LABEL org.opencontainers.image.created="2024-01-25T10:14:00Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/demux/bcl_convert/.config.vsh.yaml b/target/docker/demux/bcl_convert/.config.vsh.yaml index 3dc19aa7221..c682f50ee63 100644 --- a/target/docker/demux/bcl_convert/.config.vsh.yaml +++ b/target/docker/demux/bcl_convert/.config.vsh.yaml @@ -184,6 +184,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/demux/bcl_convert" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/demux/bcl_convert/bcl_convert" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/demux/bcl_convert/bcl_convert b/target/docker/demux/bcl_convert/bcl_convert index 76e728c25f2..3217d86dd53 100755 --- a/target/docker/demux/bcl_convert/bcl_convert +++ b/target/docker/demux/bcl_convert/bcl_convert @@ -417,9 +417,9 @@ ENTRYPOINT [] RUN : LABEL org.opencontainers.image.authors="Toni Verbeiren, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component demux bcl_convert" -LABEL org.opencontainers.image.created="2024-01-25T09:34:37Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:55Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/demux/cellranger_mkfastq/.config.vsh.yaml b/target/docker/demux/cellranger_mkfastq/.config.vsh.yaml index 5a72446e8a6..193a6e627b8 100644 --- a/target/docker/demux/cellranger_mkfastq/.config.vsh.yaml +++ b/target/docker/demux/cellranger_mkfastq/.config.vsh.yaml @@ -202,6 +202,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/demux/cellranger_mkfastq" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/demux/cellranger_mkfastq/cellranger_mkfastq" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/demux/cellranger_mkfastq/cellranger_mkfastq b/target/docker/demux/cellranger_mkfastq/cellranger_mkfastq index 17c9dbe1cce..785ee6aab85 100755 --- a/target/docker/demux/cellranger_mkfastq/cellranger_mkfastq +++ b/target/docker/demux/cellranger_mkfastq/cellranger_mkfastq @@ -416,9 +416,9 @@ ENTRYPOINT [] RUN apt-get update && apt-get upgrade -y LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Samuel D'Souza, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component demux cellranger_mkfastq" -LABEL org.opencontainers.image.created="2024-01-25T09:34:37Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:55Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/dimred/pca/.config.vsh.yaml b/target/docker/dimred/pca/.config.vsh.yaml index 32deb4ff4ba..09d7e977c32 100644 --- a/target/docker/dimred/pca/.config.vsh.yaml +++ b/target/docker/dimred/pca/.config.vsh.yaml @@ -248,6 +248,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/dimred/pca" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/dimred/pca/pca" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/dimred/pca/pca b/target/docker/dimred/pca/pca index f6e074e7b1b..028c6e95b8f 100755 --- a/target/docker/dimred/pca/pca +++ b/target/docker/dimred/pca/pca @@ -450,9 +450,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer" LABEL org.opencontainers.image.description="Companion container for running component dimred pca" -LABEL org.opencontainers.image.created="2024-01-25T09:34:36Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:57Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/dimred/umap/.config.vsh.yaml b/target/docker/dimred/umap/.config.vsh.yaml index f900ee3bc59..c67e3e8cc0b 100644 --- a/target/docker/dimred/umap/.config.vsh.yaml +++ b/target/docker/dimred/umap/.config.vsh.yaml @@ -307,6 +307,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/dimred/umap" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/dimred/umap/umap" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/dimred/umap/umap b/target/docker/dimred/umap/umap index 78b51462e02..7b88be04993 100755 --- a/target/docker/dimred/umap/umap +++ b/target/docker/dimred/umap/umap @@ -487,9 +487,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer" LABEL org.opencontainers.image.description="Companion container for running component dimred umap" -LABEL org.opencontainers.image.created="2024-01-25T09:34:36Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:57Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/download/download_file/.config.vsh.yaml b/target/docker/download/download_file/.config.vsh.yaml index 2f838681446..86a0c8b5142 100644 --- a/target/docker/download/download_file/.config.vsh.yaml +++ b/target/docker/download/download_file/.config.vsh.yaml @@ -133,6 +133,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/download/download_file" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/download/download_file/download_file" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/download/download_file/download_file b/target/docker/download/download_file/download_file index d19619d2514..c95c6155173 100755 --- a/target/docker/download/download_file/download_file +++ b/target/docker/download/download_file/download_file @@ -409,9 +409,9 @@ ENTRYPOINT [] RUN : LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component download download_file" -LABEL org.opencontainers.image.created="2024-01-25T09:34:38Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:56Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/download/sync_test_resources/.config.vsh.yaml b/target/docker/download/sync_test_resources/.config.vsh.yaml index b1ecb86c7b7..c6815328d22 100644 --- a/target/docker/download/sync_test_resources/.config.vsh.yaml +++ b/target/docker/download/sync_test_resources/.config.vsh.yaml @@ -165,6 +165,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/download/sync_test_resources" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/download/sync_test_resources/sync_test_resources" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/download/sync_test_resources/sync_test_resources b/target/docker/download/sync_test_resources/sync_test_resources index 5b618ae49e2..16ef6e1ce1c 100755 --- a/target/docker/download/sync_test_resources/sync_test_resources +++ b/target/docker/download/sync_test_resources/sync_test_resources @@ -423,9 +423,9 @@ RUN yum install -y procps && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component download sync_test_resources" -LABEL org.opencontainers.image.created="2024-01-25T09:34:38Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:55Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/files/make_params/.config.vsh.yaml b/target/docker/files/make_params/.config.vsh.yaml index ed33e180c9b..8b3297655b7 100644 --- a/target/docker/files/make_params/.config.vsh.yaml +++ b/target/docker/files/make_params/.config.vsh.yaml @@ -215,6 +215,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/files/make_params" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/files/make_params/make_params" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/files/make_params/make_params b/target/docker/files/make_params/make_params index c15a8505525..c59e9ee4a20 100755 --- a/target/docker/files/make_params/make_params +++ b/target/docker/files/make_params/make_params @@ -429,9 +429,9 @@ ENTRYPOINT [] RUN : LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component files make_params" -LABEL org.opencontainers.image.created="2024-01-25T09:34:35Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:57Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/filter/delimit_fraction/.config.vsh.yaml b/target/docker/filter/delimit_fraction/.config.vsh.yaml index 6652eada784..d16f34cc3ee 100644 --- a/target/docker/filter/delimit_fraction/.config.vsh.yaml +++ b/target/docker/filter/delimit_fraction/.config.vsh.yaml @@ -236,6 +236,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/delimit_fraction" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/delimit_fraction/delimit_fraction" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/filter/delimit_fraction/delimit_fraction b/target/docker/filter/delimit_fraction/delimit_fraction index 221013e02a4..4c18c9a5133 100755 --- a/target/docker/filter/delimit_fraction/delimit_fraction +++ b/target/docker/filter/delimit_fraction/delimit_fraction @@ -445,9 +445,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component filter delimit_fraction" -LABEL org.opencontainers.image.created="2024-01-25T09:34:38Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:56Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/filter/do_filter/.config.vsh.yaml b/target/docker/filter/do_filter/.config.vsh.yaml index 27d84aec587..3b73a95236b 100644 --- a/target/docker/filter/do_filter/.config.vsh.yaml +++ b/target/docker/filter/do_filter/.config.vsh.yaml @@ -197,6 +197,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/do_filter" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/do_filter/do_filter" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/filter/do_filter/do_filter b/target/docker/filter/do_filter/do_filter index 481764f34e2..bd18ba5afe6 100755 --- a/target/docker/filter/do_filter/do_filter +++ b/target/docker/filter/do_filter/do_filter @@ -423,9 +423,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component filter do_filter" -LABEL org.opencontainers.image.created="2024-01-25T09:34:37Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:57Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/filter/filter_with_counts/.config.vsh.yaml b/target/docker/filter/filter_with_counts/.config.vsh.yaml index 83c2a74811e..199eeea87cc 100644 --- a/target/docker/filter/filter_with_counts/.config.vsh.yaml +++ b/target/docker/filter/filter_with_counts/.config.vsh.yaml @@ -290,6 +290,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/filter_with_counts" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/filter_with_counts/filter_with_counts" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/filter/filter_with_counts/filter_with_counts b/target/docker/filter/filter_with_counts/filter_with_counts index e0667a5d6b6..68ef1ee30bd 100755 --- a/target/docker/filter/filter_with_counts/filter_with_counts +++ b/target/docker/filter/filter_with_counts/filter_with_counts @@ -463,9 +463,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component filter filter_with_counts" -LABEL org.opencontainers.image.created="2024-01-25T09:34:37Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:57Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/filter/filter_with_hvg/.config.vsh.yaml b/target/docker/filter/filter_with_hvg/.config.vsh.yaml index f4ffb396ce2..4a0d796bf0c 100644 --- a/target/docker/filter/filter_with_hvg/.config.vsh.yaml +++ b/target/docker/filter/filter_with_hvg/.config.vsh.yaml @@ -347,6 +347,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/filter_with_hvg" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/filter_with_hvg/filter_with_hvg" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/filter/filter_with_hvg/filter_with_hvg b/target/docker/filter/filter_with_hvg/filter_with_hvg index 2306b0fe45c..b0031c94d3a 100755 --- a/target/docker/filter/filter_with_hvg/filter_with_hvg +++ b/target/docker/filter/filter_with_hvg/filter_with_hvg @@ -509,9 +509,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component filter filter_with_hvg" -LABEL org.opencontainers.image.created="2024-01-25T09:34:37Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:58Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/filter/filter_with_scrublet/.config.vsh.yaml b/target/docker/filter/filter_with_scrublet/.config.vsh.yaml index d88fb42b6b1..3412282dd29 100644 --- a/target/docker/filter/filter_with_scrublet/.config.vsh.yaml +++ b/target/docker/filter/filter_with_scrublet/.config.vsh.yaml @@ -299,6 +299,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/filter_with_scrublet" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/filter_with_scrublet/filter_with_scrublet" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/filter/filter_with_scrublet/filter_with_scrublet b/target/docker/filter/filter_with_scrublet/filter_with_scrublet index 158c5c9697f..dfcfe09f054 100755 --- a/target/docker/filter/filter_with_scrublet/filter_with_scrublet +++ b/target/docker/filter/filter_with_scrublet/filter_with_scrublet @@ -484,9 +484,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component filter filter_with_scrublet" -LABEL org.opencontainers.image.created="2024-01-25T09:34:37Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:58Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/filter/remove_modality/.config.vsh.yaml b/target/docker/filter/remove_modality/.config.vsh.yaml index 24f75c1ad13..d09eeffbd9c 100644 --- a/target/docker/filter/remove_modality/.config.vsh.yaml +++ b/target/docker/filter/remove_modality/.config.vsh.yaml @@ -166,6 +166,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/remove_modality" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/remove_modality/remove_modality" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/filter/remove_modality/remove_modality b/target/docker/filter/remove_modality/remove_modality index 46fba8ebc67..47c305cbe2c 100755 --- a/target/docker/filter/remove_modality/remove_modality +++ b/target/docker/filter/remove_modality/remove_modality @@ -412,9 +412,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component filter remove_modality" -LABEL org.opencontainers.image.created="2024-01-25T09:34:38Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:57Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/filter/subset_h5mu/.config.vsh.yaml b/target/docker/filter/subset_h5mu/.config.vsh.yaml index ffd3deec89f..bfd2021f189 100644 --- a/target/docker/filter/subset_h5mu/.config.vsh.yaml +++ b/target/docker/filter/subset_h5mu/.config.vsh.yaml @@ -182,6 +182,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/subset_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/subset_h5mu/subset_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/filter/subset_h5mu/subset_h5mu b/target/docker/filter/subset_h5mu/subset_h5mu index 2327613d8a0..b43a9d3a3c1 100755 --- a/target/docker/filter/subset_h5mu/subset_h5mu +++ b/target/docker/filter/subset_h5mu/subset_h5mu @@ -418,9 +418,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component filter subset_h5mu" -LABEL org.opencontainers.image.created="2024-01-25T09:34:36Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:57Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/integrate/harmonypy/.config.vsh.yaml b/target/docker/integrate/harmonypy/.config.vsh.yaml index d81b189ad6e..ccec2aa8068 100644 --- a/target/docker/integrate/harmonypy/.config.vsh.yaml +++ b/target/docker/integrate/harmonypy/.config.vsh.yaml @@ -235,6 +235,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/harmonypy" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/harmonypy/harmonypy" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/integrate/harmonypy/harmonypy b/target/docker/integrate/harmonypy/harmonypy index 0cdb17f13d0..f5f252f0a9e 100755 --- a/target/docker/integrate/harmonypy/harmonypy +++ b/target/docker/integrate/harmonypy/harmonypy @@ -436,9 +436,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component integrate harmonypy" -LABEL org.opencontainers.image.created="2024-01-25T09:34:39Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:59Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/integrate/scanorama/.config.vsh.yaml b/target/docker/integrate/scanorama/.config.vsh.yaml index 144a0a1260e..76c83623e16 100644 --- a/target/docker/integrate/scanorama/.config.vsh.yaml +++ b/target/docker/integrate/scanorama/.config.vsh.yaml @@ -278,6 +278,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/scanorama" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/scanorama/scanorama" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/integrate/scanorama/scanorama b/target/docker/integrate/scanorama/scanorama index edb381b7a53..1d9ebd61fad 100755 --- a/target/docker/integrate/scanorama/scanorama +++ b/target/docker/integrate/scanorama/scanorama @@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component integrate scanorama" -LABEL org.opencontainers.image.created="2024-01-25T09:34:39Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:58Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/integrate/scarches/.config.vsh.yaml b/target/docker/integrate/scarches/.config.vsh.yaml index 015c3bed96b..e1b64d597ce 100644 --- a/target/docker/integrate/scarches/.config.vsh.yaml +++ b/target/docker/integrate/scarches/.config.vsh.yaml @@ -326,6 +326,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/scarches" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/scarches/scarches" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/integrate/scarches/scarches b/target/docker/integrate/scarches/scarches index ec3fafd20fb..0dfe18f77c7 100755 --- a/target/docker/integrate/scarches/scarches +++ b/target/docker/integrate/scarches/scarches @@ -481,9 +481,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Vladimir Shitov" LABEL org.opencontainers.image.description="Companion container for running component integrate scarches" -LABEL org.opencontainers.image.created="2024-01-25T09:34:39Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:57Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/integrate/scvi/.config.vsh.yaml b/target/docker/integrate/scvi/.config.vsh.yaml index e9ddfddbf1a..d52c24f5d8b 100644 --- a/target/docker/integrate/scvi/.config.vsh.yaml +++ b/target/docker/integrate/scvi/.config.vsh.yaml @@ -586,6 +586,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/scvi" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/scvi/scvi" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/integrate/scvi/scvi b/target/docker/integrate/scvi/scvi index 9f654d8d753..eda834a8674 100755 --- a/target/docker/integrate/scvi/scvi +++ b/target/docker/integrate/scvi/scvi @@ -614,9 +614,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Malte D. Luecken, Dries Schaumont, Matthias Beyens" LABEL org.opencontainers.image.description="Companion container for running component integrate scvi" -LABEL org.opencontainers.image.created="2024-01-25T09:34:38Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:58Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/integrate/totalvi/.config.vsh.yaml b/target/docker/integrate/totalvi/.config.vsh.yaml index 8f3b5e17657..deebb486875 100644 --- a/target/docker/integrate/totalvi/.config.vsh.yaml +++ b/target/docker/integrate/totalvi/.config.vsh.yaml @@ -343,6 +343,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/totalvi" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/totalvi/totalvi" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/integrate/totalvi/totalvi b/target/docker/integrate/totalvi/totalvi index 18299aab526..1fe55f29974 100755 --- a/target/docker/integrate/totalvi/totalvi +++ b/target/docker/integrate/totalvi/totalvi @@ -485,9 +485,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Vladimir Shitov" LABEL org.opencontainers.image.description="Companion container for running component integrate totalvi" -LABEL org.opencontainers.image.created="2024-01-25T09:34:39Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:58Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/interactive/run_cellxgene/.config.vsh.yaml b/target/docker/interactive/run_cellxgene/.config.vsh.yaml index 6ed5b18149b..c0c1dca36fd 100644 --- a/target/docker/interactive/run_cellxgene/.config.vsh.yaml +++ b/target/docker/interactive/run_cellxgene/.config.vsh.yaml @@ -78,6 +78,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/interactive/run_cellxgene" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/interactive/run_cellxgene/run_cellxgene" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/interactive/run_cellxgene/run_cellxgene b/target/docker/interactive/run_cellxgene/run_cellxgene index 5b501b4d0d4..47e66cbc109 100755 --- a/target/docker/interactive/run_cellxgene/run_cellxgene +++ b/target/docker/interactive/run_cellxgene/run_cellxgene @@ -400,9 +400,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "cellxgene" LABEL org.opencontainers.image.description="Companion container for running component interactive run_cellxgene" -LABEL org.opencontainers.image.created="2024-01-25T09:34:36Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:56Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/interactive/run_cirrocumulus/.config.vsh.yaml b/target/docker/interactive/run_cirrocumulus/.config.vsh.yaml index a030b0daed2..3e76e98ee2c 100644 --- a/target/docker/interactive/run_cirrocumulus/.config.vsh.yaml +++ b/target/docker/interactive/run_cirrocumulus/.config.vsh.yaml @@ -80,6 +80,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/interactive/run_cirrocumulus" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/interactive/run_cirrocumulus/run_cirrocumulus" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/interactive/run_cirrocumulus/run_cirrocumulus b/target/docker/interactive/run_cirrocumulus/run_cirrocumulus index 759b7a2f0a4..65a3c5ad76d 100755 --- a/target/docker/interactive/run_cirrocumulus/run_cirrocumulus +++ b/target/docker/interactive/run_cirrocumulus/run_cirrocumulus @@ -400,9 +400,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "requests" "aiohttp" "cirrocumulus" LABEL org.opencontainers.image.description="Companion container for running component interactive run_cirrocumulus" -LABEL org.opencontainers.image.created="2024-01-25T09:34:33Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:56Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/interpret/lianapy/.config.vsh.yaml b/target/docker/interpret/lianapy/.config.vsh.yaml index 1d4636d02da..1d24676cd7a 100644 --- a/target/docker/interpret/lianapy/.config.vsh.yaml +++ b/target/docker/interpret/lianapy/.config.vsh.yaml @@ -308,6 +308,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/interpret/lianapy" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/interpret/lianapy/lianapy" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/interpret/lianapy/lianapy b/target/docker/interpret/lianapy/lianapy index 14b886e7a52..0cd6aaf5700 100755 --- a/target/docker/interpret/lianapy/lianapy +++ b/target/docker/interpret/lianapy/lianapy @@ -470,9 +470,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Mauro Saporita, Povilas Gibas" LABEL org.opencontainers.image.description="Companion container for running component interpret lianapy" -LABEL org.opencontainers.image.created="2024-01-25T09:34:36Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:55Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/labels_transfer/knn/.config.vsh.yaml b/target/docker/labels_transfer/knn/.config.vsh.yaml index e932c92c18b..b45adbd8b4e 100644 --- a/target/docker/labels_transfer/knn/.config.vsh.yaml +++ b/target/docker/labels_transfer/knn/.config.vsh.yaml @@ -374,6 +374,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/labels_transfer/knn" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/labels_transfer/knn/knn" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/labels_transfer/knn/knn b/target/docker/labels_transfer/knn/knn index 96084796ce3..32eb89ffe31 100755 --- a/target/docker/labels_transfer/knn/knn +++ b/target/docker/labels_transfer/knn/knn @@ -468,9 +468,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Vladimir Shitov" LABEL org.opencontainers.image.description="Companion container for running component labels_transfer knn" -LABEL org.opencontainers.image.created="2024-01-25T09:34:40Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:56Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/labels_transfer/xgboost/.config.vsh.yaml b/target/docker/labels_transfer/xgboost/.config.vsh.yaml index 787630afc42..1ff97a896f4 100644 --- a/target/docker/labels_transfer/xgboost/.config.vsh.yaml +++ b/target/docker/labels_transfer/xgboost/.config.vsh.yaml @@ -589,6 +589,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/labels_transfer/xgboost" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/labels_transfer/xgboost/xgboost" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/labels_transfer/xgboost/xgboost b/target/docker/labels_transfer/xgboost/xgboost index e7d47e888fc..acbe5e5cfc8 100755 --- a/target/docker/labels_transfer/xgboost/xgboost +++ b/target/docker/labels_transfer/xgboost/xgboost @@ -595,9 +595,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Vladimir Shitov" LABEL org.opencontainers.image.description="Companion container for running component labels_transfer xgboost" -LABEL org.opencontainers.image.created="2024-01-25T09:34:40Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:56Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/mapping/bd_rhapsody/.config.vsh.yaml b/target/docker/mapping/bd_rhapsody/.config.vsh.yaml index 4c63ce1fecf..84f54badcb1 100644 --- a/target/docker/mapping/bd_rhapsody/.config.vsh.yaml +++ b/target/docker/mapping/bd_rhapsody/.config.vsh.yaml @@ -412,6 +412,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/bd_rhapsody" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/bd_rhapsody/bd_rhapsody" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/mapping/bd_rhapsody/bd_rhapsody b/target/docker/mapping/bd_rhapsody/bd_rhapsody index fec118d1ef4..6bb7983fb3e 100755 --- a/target/docker/mapping/bd_rhapsody/bd_rhapsody +++ b/target/docker/mapping/bd_rhapsody/bd_rhapsody @@ -532,9 +532,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component mapping bd_rhapsody" -LABEL org.opencontainers.image.created="2024-01-25T09:34:34Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:57Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/mapping/cellranger_count/.config.vsh.yaml b/target/docker/mapping/cellranger_count/.config.vsh.yaml index 2f967a376e7..ade2b61c89d 100644 --- a/target/docker/mapping/cellranger_count/.config.vsh.yaml +++ b/target/docker/mapping/cellranger_count/.config.vsh.yaml @@ -261,6 +261,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/cellranger_count" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/cellranger_count/cellranger_count" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/mapping/cellranger_count/cellranger_count b/target/docker/mapping/cellranger_count/cellranger_count index 9b7f90177b8..45bd87d3a16 100755 --- a/target/docker/mapping/cellranger_count/cellranger_count +++ b/target/docker/mapping/cellranger_count/cellranger_count @@ -451,9 +451,9 @@ ENTRYPOINT [] RUN apt update && apt upgrade -y LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Samuel D'Souza, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component mapping cellranger_count" -LABEL org.opencontainers.image.created="2024-01-25T09:34:36Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:57Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/mapping/cellranger_count_split/.config.vsh.yaml b/target/docker/mapping/cellranger_count_split/.config.vsh.yaml index a7cc712c4c1..18b8445f5cf 100644 --- a/target/docker/mapping/cellranger_count_split/.config.vsh.yaml +++ b/target/docker/mapping/cellranger_count_split/.config.vsh.yaml @@ -213,6 +213,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/cellranger_count_split" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/cellranger_count_split/cellranger_count_split" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/mapping/cellranger_count_split/cellranger_count_split b/target/docker/mapping/cellranger_count_split/cellranger_count_split index 6854627686f..2efd9a25590 100755 --- a/target/docker/mapping/cellranger_count_split/cellranger_count_split +++ b/target/docker/mapping/cellranger_count_split/cellranger_count_split @@ -418,9 +418,9 @@ ENTRYPOINT [] RUN apt update && apt upgrade -y LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Samuel D'Souza, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component mapping cellranger_count_split" -LABEL org.opencontainers.image.created="2024-01-25T09:34:34Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:55Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/mapping/cellranger_multi/.config.vsh.yaml b/target/docker/mapping/cellranger_multi/.config.vsh.yaml index b34f01a3d42..3829e2bcd8d 100644 --- a/target/docker/mapping/cellranger_multi/.config.vsh.yaml +++ b/target/docker/mapping/cellranger_multi/.config.vsh.yaml @@ -418,6 +418,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/cellranger_multi" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/cellranger_multi/cellranger_multi" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/mapping/cellranger_multi/cellranger_multi b/target/docker/mapping/cellranger_multi/cellranger_multi index 683a027902d..16128636037 100755 --- a/target/docker/mapping/cellranger_multi/cellranger_multi +++ b/target/docker/mapping/cellranger_multi/cellranger_multi @@ -532,9 +532,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt, Dries De Maeyer" LABEL org.opencontainers.image.description="Companion container for running component mapping cellranger_multi" -LABEL org.opencontainers.image.created="2024-01-25T09:34:36Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:55Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/mapping/htseq_count/.config.vsh.yaml b/target/docker/mapping/htseq_count/.config.vsh.yaml index d2c11a6a7f0..1bd957c81c8 100644 --- a/target/docker/mapping/htseq_count/.config.vsh.yaml +++ b/target/docker/mapping/htseq_count/.config.vsh.yaml @@ -413,6 +413,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/htseq_count" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/htseq_count/htseq_count" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/mapping/htseq_count/htseq_count b/target/docker/mapping/htseq_count/htseq_count index d4a4a001158..2399b9f2a37 100755 --- a/target/docker/mapping/htseq_count/htseq_count +++ b/target/docker/mapping/htseq_count/htseq_count @@ -526,9 +526,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Angela Oliveira Pisco" LABEL org.opencontainers.image.description="Companion container for running component mapping htseq_count" -LABEL org.opencontainers.image.created="2024-01-25T09:34:35Z" +LABEL org.opencontainers.image.created="2024-01-25T10:14:00Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/mapping/htseq_count_to_h5mu/.config.vsh.yaml b/target/docker/mapping/htseq_count_to_h5mu/.config.vsh.yaml index 04cb80eda68..f08aa9ac37f 100644 --- a/target/docker/mapping/htseq_count_to_h5mu/.config.vsh.yaml +++ b/target/docker/mapping/htseq_count_to_h5mu/.config.vsh.yaml @@ -204,6 +204,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/htseq_count_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu b/target/docker/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu index 4d39bdd3cc6..f75d95ef0dd 100755 --- a/target/docker/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu +++ b/target/docker/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu @@ -421,9 +421,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Angela Oliveira Pisco" LABEL org.opencontainers.image.description="Companion container for running component mapping htseq_count_to_h5mu" -LABEL org.opencontainers.image.created="2024-01-25T09:34:33Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:59Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/mapping/multi_star/.config.vsh.yaml b/target/docker/mapping/multi_star/.config.vsh.yaml index e84ab8a952c..e66b519f23d 100644 --- a/target/docker/mapping/multi_star/.config.vsh.yaml +++ b/target/docker/mapping/multi_star/.config.vsh.yaml @@ -3075,6 +3075,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/multi_star" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/multi_star/multi_star" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/mapping/multi_star/multi_star b/target/docker/mapping/multi_star/multi_star index a31b316c36f..236aecae1eb 100755 --- a/target/docker/mapping/multi_star/multi_star +++ b/target/docker/mapping/multi_star/multi_star @@ -1861,9 +1861,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component mapping multi_star" -LABEL org.opencontainers.image.created="2024-01-25T09:34:35Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:56Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/mapping/multi_star_to_h5mu/.config.vsh.yaml b/target/docker/mapping/multi_star_to_h5mu/.config.vsh.yaml index 5c23240314f..c0f10e359c8 100644 --- a/target/docker/mapping/multi_star_to_h5mu/.config.vsh.yaml +++ b/target/docker/mapping/multi_star_to_h5mu/.config.vsh.yaml @@ -174,6 +174,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/multi_star_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/multi_star_to_h5mu/multi_star_to_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/mapping/multi_star_to_h5mu/multi_star_to_h5mu b/target/docker/mapping/multi_star_to_h5mu/multi_star_to_h5mu index 4ccc6143519..d9c9fb15726 100755 --- a/target/docker/mapping/multi_star_to_h5mu/multi_star_to_h5mu +++ b/target/docker/mapping/multi_star_to_h5mu/multi_star_to_h5mu @@ -410,9 +410,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Angela Oliveira Pisco" LABEL org.opencontainers.image.description="Companion container for running component mapping multi_star_to_h5mu" -LABEL org.opencontainers.image.created="2024-01-25T09:34:35Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:55Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/mapping/samtools_sort/.config.vsh.yaml b/target/docker/mapping/samtools_sort/.config.vsh.yaml index cd0bd9b3107..3aec09b023a 100644 --- a/target/docker/mapping/samtools_sort/.config.vsh.yaml +++ b/target/docker/mapping/samtools_sort/.config.vsh.yaml @@ -265,6 +265,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/samtools_sort" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/samtools_sort/samtools_sort" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/mapping/samtools_sort/samtools_sort b/target/docker/mapping/samtools_sort/samtools_sort index ce75cf11455..a85d26a34ed 100755 --- a/target/docker/mapping/samtools_sort/samtools_sort +++ b/target/docker/mapping/samtools_sort/samtools_sort @@ -466,9 +466,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Angela Oliveira Pisco" LABEL org.opencontainers.image.description="Companion container for running component mapping samtools_sort" -LABEL org.opencontainers.image.created="2024-01-25T09:34:34Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:55Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/mapping/star_align/.config.vsh.yaml b/target/docker/mapping/star_align/.config.vsh.yaml index 1b3cbeb47d2..1787020a5c0 100644 --- a/target/docker/mapping/star_align/.config.vsh.yaml +++ b/target/docker/mapping/star_align/.config.vsh.yaml @@ -2530,6 +2530,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/star_align" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/star_align/star_align" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/mapping/star_align/star_align b/target/docker/mapping/star_align/star_align index 3e82c05ea3a..b05bbaaa1e4 100755 --- a/target/docker/mapping/star_align/star_align +++ b/target/docker/mapping/star_align/star_align @@ -1789,9 +1789,9 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component mapping star_align" -LABEL org.opencontainers.image.created="2024-01-25T09:34:34Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:56Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/mapping/star_align_v273a/.config.vsh.yaml b/target/docker/mapping/star_align_v273a/.config.vsh.yaml index 3eab894b428..15a0341df41 100644 --- a/target/docker/mapping/star_align_v273a/.config.vsh.yaml +++ b/target/docker/mapping/star_align_v273a/.config.vsh.yaml @@ -2530,6 +2530,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/star_align_v273a" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/star_align_v273a/star_align_v273a" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/mapping/star_align_v273a/star_align_v273a b/target/docker/mapping/star_align_v273a/star_align_v273a index bf9c761af3b..3e3d0f0f339 100755 --- a/target/docker/mapping/star_align_v273a/star_align_v273a +++ b/target/docker/mapping/star_align_v273a/star_align_v273a @@ -1789,9 +1789,9 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component mapping star_align_v273a" -LABEL org.opencontainers.image.created="2024-01-25T09:34:35Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:56Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/mapping/star_build_reference/.config.vsh.yaml b/target/docker/mapping/star_build_reference/.config.vsh.yaml index 1bd632065ff..27a4226e047 100644 --- a/target/docker/mapping/star_build_reference/.config.vsh.yaml +++ b/target/docker/mapping/star_build_reference/.config.vsh.yaml @@ -185,6 +185,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/star_build_reference" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/star_build_reference/star_build_reference" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/mapping/star_build_reference/star_build_reference b/target/docker/mapping/star_build_reference/star_build_reference index 15d8b032cae..7e74bc45069 100755 --- a/target/docker/mapping/star_build_reference/star_build_reference +++ b/target/docker/mapping/star_build_reference/star_build_reference @@ -437,9 +437,9 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component mapping star_build_reference" -LABEL org.opencontainers.image.created="2024-01-25T09:34:36Z" +LABEL org.opencontainers.image.created="2024-01-25T10:14:00Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/metadata/add_id/.config.vsh.yaml b/target/docker/metadata/add_id/.config.vsh.yaml index 3cde5a0ed27..d8140155307 100644 --- a/target/docker/metadata/add_id/.config.vsh.yaml +++ b/target/docker/metadata/add_id/.config.vsh.yaml @@ -192,6 +192,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/add_id" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/add_id/add_id" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/metadata/add_id/add_id b/target/docker/metadata/add_id/add_id index e0b8db8eb2f..663e58f4349 100755 --- a/target/docker/metadata/add_id/add_id +++ b/target/docker/metadata/add_id/add_id @@ -422,9 +422,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component metadata add_id" -LABEL org.opencontainers.image.created="2024-01-25T09:34:35Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:59Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/metadata/grep_annotation_column/.config.vsh.yaml b/target/docker/metadata/grep_annotation_column/.config.vsh.yaml index 3b802a3dd25..594bfcfaa9e 100644 --- a/target/docker/metadata/grep_annotation_column/.config.vsh.yaml +++ b/target/docker/metadata/grep_annotation_column/.config.vsh.yaml @@ -239,6 +239,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/grep_annotation_column" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/grep_annotation_column/grep_annotation_column" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/metadata/grep_annotation_column/grep_annotation_column b/target/docker/metadata/grep_annotation_column/grep_annotation_column index 440125064ab..39e2db2b16d 100755 --- a/target/docker/metadata/grep_annotation_column/grep_annotation_column +++ b/target/docker/metadata/grep_annotation_column/grep_annotation_column @@ -448,9 +448,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component metadata grep_annotation_column" -LABEL org.opencontainers.image.created="2024-01-25T09:34:36Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:58Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/metadata/join_csv/.config.vsh.yaml b/target/docker/metadata/join_csv/.config.vsh.yaml index 09f92447805..beac67bda0a 100644 --- a/target/docker/metadata/join_csv/.config.vsh.yaml +++ b/target/docker/metadata/join_csv/.config.vsh.yaml @@ -224,6 +224,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/join_csv" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/join_csv/join_csv" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/metadata/join_csv/join_csv b/target/docker/metadata/join_csv/join_csv index 509e6e596f6..5fac93215fd 100755 --- a/target/docker/metadata/join_csv/join_csv +++ b/target/docker/metadata/join_csv/join_csv @@ -438,9 +438,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component metadata join_csv" -LABEL org.opencontainers.image.created="2024-01-25T09:34:35Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:59Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/metadata/join_uns_to_obs/.config.vsh.yaml b/target/docker/metadata/join_uns_to_obs/.config.vsh.yaml index 26c1867d57d..6efbf4fd030 100644 --- a/target/docker/metadata/join_uns_to_obs/.config.vsh.yaml +++ b/target/docker/metadata/join_uns_to_obs/.config.vsh.yaml @@ -166,6 +166,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/join_uns_to_obs" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/join_uns_to_obs/join_uns_to_obs" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/metadata/join_uns_to_obs/join_uns_to_obs b/target/docker/metadata/join_uns_to_obs/join_uns_to_obs index 6324a1f9ef6..e59ad3a0701 100755 --- a/target/docker/metadata/join_uns_to_obs/join_uns_to_obs +++ b/target/docker/metadata/join_uns_to_obs/join_uns_to_obs @@ -413,9 +413,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "mudata~=0.2.3" "anndata~=0.9.1" LABEL org.opencontainers.image.description="Companion container for running component metadata join_uns_to_obs" -LABEL org.opencontainers.image.created="2024-01-25T09:34:35Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:59Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/metadata/move_obsm_to_obs/.config.vsh.yaml b/target/docker/metadata/move_obsm_to_obs/.config.vsh.yaml index 99d5fff1f86..121582d4551 100644 --- a/target/docker/metadata/move_obsm_to_obs/.config.vsh.yaml +++ b/target/docker/metadata/move_obsm_to_obs/.config.vsh.yaml @@ -187,6 +187,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/move_obsm_to_obs" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/move_obsm_to_obs/move_obsm_to_obs" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/metadata/move_obsm_to_obs/move_obsm_to_obs b/target/docker/metadata/move_obsm_to_obs/move_obsm_to_obs index f10af344862..9a91bbbad0d 100755 --- a/target/docker/metadata/move_obsm_to_obs/move_obsm_to_obs +++ b/target/docker/metadata/move_obsm_to_obs/move_obsm_to_obs @@ -421,9 +421,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component metadata move_obsm_to_obs" -LABEL org.opencontainers.image.created="2024-01-25T09:34:35Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:59Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/neighbors/bbknn/.config.vsh.yaml b/target/docker/neighbors/bbknn/.config.vsh.yaml index 4259496ef6b..87dff641d9b 100644 --- a/target/docker/neighbors/bbknn/.config.vsh.yaml +++ b/target/docker/neighbors/bbknn/.config.vsh.yaml @@ -284,6 +284,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/neighbors/bbknn" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/neighbors/bbknn/bbknn" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/neighbors/bbknn/bbknn b/target/docker/neighbors/bbknn/bbknn index 8f0e98da007..12cada2b7c8 100755 --- a/target/docker/neighbors/bbknn/bbknn +++ b/target/docker/neighbors/bbknn/bbknn @@ -463,9 +463,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component neighbors bbknn" -LABEL org.opencontainers.image.created="2024-01-25T09:34:36Z" +LABEL org.opencontainers.image.created="2024-01-25T10:14:00Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/neighbors/find_neighbors/.config.vsh.yaml b/target/docker/neighbors/find_neighbors/.config.vsh.yaml index 07c05ebb290..4aaa7d85d25 100644 --- a/target/docker/neighbors/find_neighbors/.config.vsh.yaml +++ b/target/docker/neighbors/find_neighbors/.config.vsh.yaml @@ -304,6 +304,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/neighbors/find_neighbors" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/neighbors/find_neighbors/find_neighbors" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/neighbors/find_neighbors/find_neighbors b/target/docker/neighbors/find_neighbors/find_neighbors index 7b3792f8da6..110a9f5995e 100755 --- a/target/docker/neighbors/find_neighbors/find_neighbors +++ b/target/docker/neighbors/find_neighbors/find_neighbors @@ -468,9 +468,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component neighbors find_neighbors" -LABEL org.opencontainers.image.created="2024-01-25T09:34:39Z" +LABEL org.opencontainers.image.created="2024-01-25T10:14:00Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/process_10xh5/filter_10xh5/.config.vsh.yaml b/target/docker/process_10xh5/filter_10xh5/.config.vsh.yaml index 61d288928ae..44bf64da637 100644 --- a/target/docker/process_10xh5/filter_10xh5/.config.vsh.yaml +++ b/target/docker/process_10xh5/filter_10xh5/.config.vsh.yaml @@ -190,6 +190,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/process_10xh5/filter_10xh5" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/process_10xh5/filter_10xh5/filter_10xh5" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/process_10xh5/filter_10xh5/filter_10xh5 b/target/docker/process_10xh5/filter_10xh5/filter_10xh5 index 6398d8a53da..c8c56f847ba 100755 --- a/target/docker/process_10xh5/filter_10xh5/filter_10xh5 +++ b/target/docker/process_10xh5/filter_10xh5/filter_10xh5 @@ -431,9 +431,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component process_10xh5 filter_10xh5" -LABEL org.opencontainers.image.created="2024-01-25T09:34:36Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:55Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/qc/calculate_qc_metrics/.config.vsh.yaml b/target/docker/qc/calculate_qc_metrics/.config.vsh.yaml index 45934a62923..8e31355e8d3 100644 --- a/target/docker/qc/calculate_qc_metrics/.config.vsh.yaml +++ b/target/docker/qc/calculate_qc_metrics/.config.vsh.yaml @@ -230,6 +230,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/qc/calculate_qc_metrics" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/qc/calculate_qc_metrics/calculate_qc_metrics" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/qc/calculate_qc_metrics/calculate_qc_metrics b/target/docker/qc/calculate_qc_metrics/calculate_qc_metrics index 13fa9cc0f50..ac2dc69a960 100755 --- a/target/docker/qc/calculate_qc_metrics/calculate_qc_metrics +++ b/target/docker/qc/calculate_qc_metrics/calculate_qc_metrics @@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component qc calculate_qc_metrics" -LABEL org.opencontainers.image.created="2024-01-25T09:34:35Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:56Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/qc/fastqc/.config.vsh.yaml b/target/docker/qc/fastqc/.config.vsh.yaml index 09197a35f1a..5b9bc7c206c 100644 --- a/target/docker/qc/fastqc/.config.vsh.yaml +++ b/target/docker/qc/fastqc/.config.vsh.yaml @@ -151,6 +151,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/qc/fastqc" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/qc/fastqc/fastqc" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/qc/fastqc/fastqc b/target/docker/qc/fastqc/fastqc index 27bc2d0ff37..7cfbcb08d90 100755 --- a/target/docker/qc/fastqc/fastqc +++ b/target/docker/qc/fastqc/fastqc @@ -410,9 +410,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component qc fastqc" -LABEL org.opencontainers.image.created="2024-01-25T09:34:35Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:56Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/qc/multiqc/.config.vsh.yaml b/target/docker/qc/multiqc/.config.vsh.yaml index cd987bca607..29ac6ccd722 100644 --- a/target/docker/qc/multiqc/.config.vsh.yaml +++ b/target/docker/qc/multiqc/.config.vsh.yaml @@ -135,6 +135,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/qc/multiqc" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/qc/multiqc/multiqc" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/qc/multiqc/multiqc b/target/docker/qc/multiqc/multiqc index 475f9f343a4..78551b56046 100755 --- a/target/docker/qc/multiqc/multiqc +++ b/target/docker/qc/multiqc/multiqc @@ -403,9 +403,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "multiqc" LABEL org.opencontainers.image.description="Companion container for running component qc multiqc" -LABEL org.opencontainers.image.created="2024-01-25T09:34:35Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:56Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/query/cellxgene_census/.config.vsh.yaml b/target/docker/query/cellxgene_census/.config.vsh.yaml index cbee9b478e2..5d70f14e279 100644 --- a/target/docker/query/cellxgene_census/.config.vsh.yaml +++ b/target/docker/query/cellxgene_census/.config.vsh.yaml @@ -255,6 +255,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/query/cellxgene_census" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/query/cellxgene_census/cellxgene_census" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/query/cellxgene_census/cellxgene_census b/target/docker/query/cellxgene_census/cellxgene_census index 3a387557002..216f6adccf7 100755 --- a/target/docker/query/cellxgene_census/cellxgene_census +++ b/target/docker/query/cellxgene_census/cellxgene_census @@ -452,9 +452,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Matthias Beyens, Dries De Maeyer" LABEL org.opencontainers.image.description="Companion container for running component query cellxgene_census" -LABEL org.opencontainers.image.created="2024-01-25T09:34:37Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:59Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/reference/build_bdrhap_reference/.config.vsh.yaml b/target/docker/reference/build_bdrhap_reference/.config.vsh.yaml index af18cb5bac5..b5a7481b59d 100644 --- a/target/docker/reference/build_bdrhap_reference/.config.vsh.yaml +++ b/target/docker/reference/build_bdrhap_reference/.config.vsh.yaml @@ -181,6 +181,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/reference/build_bdrhap_reference" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/reference/build_bdrhap_reference/build_bdrhap_reference" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/reference/build_bdrhap_reference/build_bdrhap_reference b/target/docker/reference/build_bdrhap_reference/build_bdrhap_reference index 5a267873050..e5be7c7e6c9 100755 --- a/target/docker/reference/build_bdrhap_reference/build_bdrhap_reference +++ b/target/docker/reference/build_bdrhap_reference/build_bdrhap_reference @@ -406,9 +406,9 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component reference build_bdrhap_reference" -LABEL org.opencontainers.image.created="2024-01-25T09:34:39Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:59Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/reference/build_cellranger_reference/.config.vsh.yaml b/target/docker/reference/build_cellranger_reference/.config.vsh.yaml index 83f4b4e6e2a..37e084ee631 100644 --- a/target/docker/reference/build_cellranger_reference/.config.vsh.yaml +++ b/target/docker/reference/build_cellranger_reference/.config.vsh.yaml @@ -182,6 +182,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/reference/build_cellranger_reference" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/reference/build_cellranger_reference/build_cellranger_reference" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/reference/build_cellranger_reference/build_cellranger_reference b/target/docker/reference/build_cellranger_reference/build_cellranger_reference index 07306ff7b1f..b9488372256 100755 --- a/target/docker/reference/build_cellranger_reference/build_cellranger_reference +++ b/target/docker/reference/build_cellranger_reference/build_cellranger_reference @@ -407,9 +407,9 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component reference build_cellranger_reference" -LABEL org.opencontainers.image.created="2024-01-25T09:34:39Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:58Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/reference/make_reference/.config.vsh.yaml b/target/docker/reference/make_reference/.config.vsh.yaml index 9993a251a56..96b46117140 100644 --- a/target/docker/reference/make_reference/.config.vsh.yaml +++ b/target/docker/reference/make_reference/.config.vsh.yaml @@ -207,6 +207,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/reference/make_reference" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/reference/make_reference/make_reference" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/reference/make_reference/make_reference b/target/docker/reference/make_reference/make_reference index 10543275bfd..e42d725f88d 100755 --- a/target/docker/reference/make_reference/make_reference +++ b/target/docker/reference/make_reference/make_reference @@ -428,9 +428,9 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component reference make_reference" -LABEL org.opencontainers.image.created="2024-01-25T09:34:40Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:58Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/report/mermaid/.config.vsh.yaml b/target/docker/report/mermaid/.config.vsh.yaml index a01da2fde71..37e563fa2ed 100644 --- a/target/docker/report/mermaid/.config.vsh.yaml +++ b/target/docker/report/mermaid/.config.vsh.yaml @@ -180,6 +180,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/report/mermaid" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/report/mermaid/mermaid" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/report/mermaid/mermaid b/target/docker/report/mermaid/mermaid index 2a40317fd7d..77fec013964 100755 --- a/target/docker/report/mermaid/mermaid +++ b/target/docker/report/mermaid/mermaid @@ -423,9 +423,9 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Dries De Maeyer" LABEL org.opencontainers.image.description="Companion container for running component report mermaid" -LABEL org.opencontainers.image.created="2024-01-25T09:34:38Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:57Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/transfer/publish/.config.vsh.yaml b/target/docker/transfer/publish/.config.vsh.yaml index 66843b9f46f..d52f774e80f 100644 --- a/target/docker/transfer/publish/.config.vsh.yaml +++ b/target/docker/transfer/publish/.config.vsh.yaml @@ -120,6 +120,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/transfer/publish" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/transfer/publish/publish" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/transfer/publish/publish b/target/docker/transfer/publish/publish index de6f9418b8f..d6f5f305068 100755 --- a/target/docker/transfer/publish/publish +++ b/target/docker/transfer/publish/publish @@ -395,9 +395,9 @@ ENTRYPOINT [] RUN : LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component transfer publish" -LABEL org.opencontainers.image.created="2024-01-25T09:34:36Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:59Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/transform/clr/.config.vsh.yaml b/target/docker/transform/clr/.config.vsh.yaml index 9d25bfd6eed..3943f5cddda 100644 --- a/target/docker/transform/clr/.config.vsh.yaml +++ b/target/docker/transform/clr/.config.vsh.yaml @@ -183,6 +183,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/clr" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/clr/clr" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/transform/clr/clr b/target/docker/transform/clr/clr index 99e534bec10..65f8f44ee05 100755 --- a/target/docker/transform/clr/clr +++ b/target/docker/transform/clr/clr @@ -417,9 +417,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component transform clr" -LABEL org.opencontainers.image.created="2024-01-25T09:34:35Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:54Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/transform/delete_layer/.config.vsh.yaml b/target/docker/transform/delete_layer/.config.vsh.yaml index 1e63bf6c105..3ee51374380 100644 --- a/target/docker/transform/delete_layer/.config.vsh.yaml +++ b/target/docker/transform/delete_layer/.config.vsh.yaml @@ -191,6 +191,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/delete_layer" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/delete_layer/delete_layer" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/transform/delete_layer/delete_layer b/target/docker/transform/delete_layer/delete_layer index ce7953fe743..326a2403ebb 100755 --- a/target/docker/transform/delete_layer/delete_layer +++ b/target/docker/transform/delete_layer/delete_layer @@ -421,9 +421,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component transform delete_layer" -LABEL org.opencontainers.image.created="2024-01-25T09:34:34Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:55Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/transform/log1p/.config.vsh.yaml b/target/docker/transform/log1p/.config.vsh.yaml index 5c46f5e6c4a..2399737e5c9 100644 --- a/target/docker/transform/log1p/.config.vsh.yaml +++ b/target/docker/transform/log1p/.config.vsh.yaml @@ -220,6 +220,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/log1p" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/log1p/log1p" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/transform/log1p/log1p b/target/docker/transform/log1p/log1p index 0987c7f7225..545cf35f8bd 100755 --- a/target/docker/transform/log1p/log1p +++ b/target/docker/transform/log1p/log1p @@ -427,9 +427,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component transform log1p" -LABEL org.opencontainers.image.created="2024-01-25T09:34:35Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:55Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/transform/normalize_total/.config.vsh.yaml b/target/docker/transform/normalize_total/.config.vsh.yaml index 8288d116627..251aa7c1ece 100644 --- a/target/docker/transform/normalize_total/.config.vsh.yaml +++ b/target/docker/transform/normalize_total/.config.vsh.yaml @@ -237,6 +237,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/normalize_total" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/normalize_total/normalize_total" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/transform/normalize_total/normalize_total b/target/docker/transform/normalize_total/normalize_total index 21f4d7d3e52..bb35c7c2a20 100755 --- a/target/docker/transform/normalize_total/normalize_total +++ b/target/docker/transform/normalize_total/normalize_total @@ -445,9 +445,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component transform normalize_total" -LABEL org.opencontainers.image.created="2024-01-25T09:34:34Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:59Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/transform/regress_out/.config.vsh.yaml b/target/docker/transform/regress_out/.config.vsh.yaml index 85695b2f282..855d304927a 100644 --- a/target/docker/transform/regress_out/.config.vsh.yaml +++ b/target/docker/transform/regress_out/.config.vsh.yaml @@ -190,6 +190,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/regress_out" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/regress_out/regress_out" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/transform/regress_out/regress_out b/target/docker/transform/regress_out/regress_out index 2618e7d4665..847f0f0405f 100755 --- a/target/docker/transform/regress_out/regress_out +++ b/target/docker/transform/regress_out/regress_out @@ -423,9 +423,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component transform regress_out" -LABEL org.opencontainers.image.created="2024-01-25T09:34:35Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:59Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/transform/scale/.config.vsh.yaml b/target/docker/transform/scale/.config.vsh.yaml index 0f0d5975ead..d41bde0466b 100644 --- a/target/docker/transform/scale/.config.vsh.yaml +++ b/target/docker/transform/scale/.config.vsh.yaml @@ -200,6 +200,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/scale" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/scale/scale" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/transform/scale/scale b/target/docker/transform/scale/scale index 14868312875..ffa4c94baef 100755 --- a/target/docker/transform/scale/scale +++ b/target/docker/transform/scale/scale @@ -424,9 +424,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component transform scale" -LABEL org.opencontainers.image.created="2024-01-25T09:34:34Z" +LABEL org.opencontainers.image.created="2024-01-25T10:14:00Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/velocity/scvelo/.config.vsh.yaml b/target/docker/velocity/scvelo/.config.vsh.yaml index 7dff4ed04a6..15437092c10 100644 --- a/target/docker/velocity/scvelo/.config.vsh.yaml +++ b/target/docker/velocity/scvelo/.config.vsh.yaml @@ -271,6 +271,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/velocity/scvelo" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/velocity/scvelo/scvelo" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/velocity/scvelo/scvelo b/target/docker/velocity/scvelo/scvelo index ccb05e170b5..21662a9f061 100755 --- a/target/docker/velocity/scvelo/scvelo +++ b/target/docker/velocity/scvelo/scvelo @@ -464,9 +464,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component velocity scvelo" -LABEL org.opencontainers.image.created="2024-01-25T09:34:34Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:57Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/docker/velocity/velocyto/.config.vsh.yaml b/target/docker/velocity/velocyto/.config.vsh.yaml index 7857f7979a3..ab3aaef9215 100644 --- a/target/docker/velocity/velocyto/.config.vsh.yaml +++ b/target/docker/velocity/velocyto/.config.vsh.yaml @@ -220,6 +220,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/velocity/velocyto" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/velocity/velocyto/velocyto" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/docker/velocity/velocyto/velocyto b/target/docker/velocity/velocyto/velocyto index 788ad30fa25..d01f23cb3ed 100755 --- a/target/docker/velocity/velocyto/velocyto +++ b/target/docker/velocity/velocyto/velocyto @@ -430,9 +430,9 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component velocity velocyto" -LABEL org.opencontainers.image.created="2024-01-25T09:34:34Z" +LABEL org.opencontainers.image.created="2024-01-25T10:13:58Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="a98b37524a0b7ccc2693db3e2df30d77f7230fd8" +LABEL org.opencontainers.image.revision="827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" LABEL org.opencontainers.image.version="0.12.3" VIASHDOCKER diff --git a/target/native/compression/compress_h5mu/.config.vsh.yaml b/target/native/compression/compress_h5mu/.config.vsh.yaml index 0cd9ca43069..796957e4b21 100644 --- a/target/native/compression/compress_h5mu/.config.vsh.yaml +++ b/target/native/compression/compress_h5mu/.config.vsh.yaml @@ -162,6 +162,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/compression/compress_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/native/compression/compress_h5mu/compress_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/native/compression/tar_extract/.config.vsh.yaml b/target/native/compression/tar_extract/.config.vsh.yaml index 5ccd5ad301a..54961584036 100644 --- a/target/native/compression/tar_extract/.config.vsh.yaml +++ b/target/native/compression/tar_extract/.config.vsh.yaml @@ -101,6 +101,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/compression/tar_extract" executable: "/home/runner/work/openpipeline/openpipeline/target/native/compression/tar_extract/tar_extract" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/native/dataflow/concat/.config.vsh.yaml b/target/native/dataflow/concat/.config.vsh.yaml index ac3bccd0e26..a8c84537551 100644 --- a/target/native/dataflow/concat/.config.vsh.yaml +++ b/target/native/dataflow/concat/.config.vsh.yaml @@ -217,6 +217,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/dataflow/concat" executable: "/home/runner/work/openpipeline/openpipeline/target/native/dataflow/concat/concat" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/native/dataflow/concat/concat b/target/native/dataflow/concat/concat index f4b6b53dc43..bf13d879091 100755 --- a/target/native/dataflow/concat/concat +++ b/target/native/dataflow/concat/concat @@ -675,20 +675,19 @@ def any_row_contains_duplicate_values(n_processes: int, frame: pd.DataFrame) -> is_duplicated = pool.map(nunique, iter(numpy_array)) return any(is_duplicated) -def concatenate_matrices(n_processes: int, input_ids: tuple[str], matrices: Iterable[pd.DataFrame], align_to: pd.Index | None) \\ +def concatenate_matrices(n_processes: int, matrices: dict[str, pd.DataFrame], align_to: pd.Index | None) \\ -> tuple[dict[str, pd.DataFrame], pd.DataFrame | None, dict[str, pd.core.dtypes.dtypes.Dtype]]: """ Merge matrices by combining columns that have the same name. Columns that contain conflicting values (e.i. the columns have different values), are not merged, but instead moved to a new dataframe. """ - column_names = set(column_name for var in matrices for column_name in var) + column_names = set(column_name for var in matrices.values() for column_name in var) logger.debug('Trying to concatenate columns: %s.', ",".join(column_names)) if not column_names: return {}, pd.DataFrame(index=align_to) conflicts, concatenated_matrix = \\ split_conflicts_and_concatenated_columns(n_processes, - input_ids, matrices, column_names, align_to) @@ -705,8 +704,7 @@ def get_first_non_na_value_vector(df): return pd.Series(numpy_arr.ravel()[flat_index], index=df.index, name=df.columns[0]) def split_conflicts_and_concatenated_columns(n_processes: int, - input_ids: tuple[str], - matrices: Iterable[pd.DataFrame], + matrices: dict[str, pd.DataFrame], column_names: Iterable[str], align_to: pd.Index | None = None) -> \\ tuple[dict[str, pd.DataFrame], pd.DataFrame]: @@ -720,14 +718,17 @@ def split_conflicts_and_concatenated_columns(n_processes: int, conflicts = {} concatenated_matrix = [] for column_name in column_names: - columns = [var[column_name] for var in matrices if column_name in var] + columns = {input_id: var[column_name] + for input_id, var in matrices.items() + if column_name in var} assert columns, "Some columns should have been found." - concatenated_columns = pd.concat(columns, axis=1, join="outer", sort=False) + concatenated_columns = pd.concat(columns.values(), axis=1, + join="outer", sort=False) if any_row_contains_duplicate_values(n_processes, concatenated_columns): - concatenated_columns.columns = input_ids + concatenated_columns.columns = columns.keys() # Use the sample id as column name if align_to is not None: concatenated_columns = concatenated_columns.reindex(align_to, copy=False) - conflicts[f'conflict_{column_name}'] = concatenated_columns + conflicts[f'conflict_{column_name}'] = concatenated_columns else: unique_values = get_first_non_na_value_vector(concatenated_columns) concatenated_matrix.append(unique_values) @@ -761,7 +762,7 @@ def cast_to_writeable_dtype(result: pd.DataFrame) -> pd.DataFrame: result[obj_col] = result[obj_col].where(result[obj_col].isna(), result[obj_col].astype(str)).astype('category') return result -def split_conflicts_modalities(n_processes: int, input_ids: tuple[str], samples: Iterable[anndata.AnnData], output: anndata.AnnData) \\ +def split_conflicts_modalities(n_processes: int, samples: dict[str, anndata.AnnData], output: anndata.AnnData) \\ -> anndata.AnnData: """ Merge .var and .obs matrices of the anndata objects. Columns are merged @@ -771,10 +772,10 @@ def split_conflicts_modalities(n_processes: int, input_ids: tuple[str], samples: """ matrices_to_parse = ("var", "obs") for matrix_name in matrices_to_parse: - matrices = [getattr(sample, matrix_name) for sample in samples] + matrices = {sample_id: getattr(sample, matrix_name) for sample_id, sample in samples.items()} output_index = getattr(output, matrix_name).index align_to = output_index if matrix_name == "var" else None - conflicts, concatenated_matrix = concatenate_matrices(n_processes, input_ids, matrices, align_to) + conflicts, concatenated_matrix = concatenate_matrices(n_processes, matrices, align_to) if concatenated_matrix.empty: concatenated_matrix.index = output_index # Write the conflicts to the output @@ -795,20 +796,20 @@ def concatenate_modality(n_processes: int, mod: str, input_files: Iterable[str | } other_axis_mode_to_apply = concat_modes.get(other_axis_mode, other_axis_mode) - mod_data = [] - for input_file in input_files: + mod_data = {} + for input_id, input_file in zip(input_ids, input_files): try: - mod_data.append(mu.read_h5ad(input_file, mod=mod)) + mod_data[input_id] = mu.read_h5ad(input_file, mod=mod) except KeyError as e: # Modality does not exist for this sample, skip it if f"Unable to open object '{mod}' doesn't exist" not in str(e): raise e pass - check_observations_unique(mod_data) + check_observations_unique(mod_data.values()) - concatenated_data = anndata.concat(mod_data, join='outer', merge=other_axis_mode_to_apply) + concatenated_data = anndata.concat(mod_data.values(), join='outer', merge=other_axis_mode_to_apply) if other_axis_mode == "move": - concatenated_data = split_conflicts_modalities(n_processes, input_ids, mod_data, concatenated_data) + concatenated_data = split_conflicts_modalities(n_processes, mod_data, concatenated_data) return concatenated_data diff --git a/target/native/dataflow/merge/.config.vsh.yaml b/target/native/dataflow/merge/.config.vsh.yaml index 07e8930960d..ae5c396225e 100644 --- a/target/native/dataflow/merge/.config.vsh.yaml +++ b/target/native/dataflow/merge/.config.vsh.yaml @@ -170,6 +170,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/dataflow/merge" executable: "/home/runner/work/openpipeline/openpipeline/target/native/dataflow/merge/merge" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/native/dataflow/split_modalities/.config.vsh.yaml b/target/native/dataflow/split_modalities/.config.vsh.yaml index 045c4fae560..9e246e14997 100644 --- a/target/native/dataflow/split_modalities/.config.vsh.yaml +++ b/target/native/dataflow/split_modalities/.config.vsh.yaml @@ -209,6 +209,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/dataflow/split_modalities" executable: "/home/runner/work/openpipeline/openpipeline/target/native/dataflow/split_modalities/split_modalities" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/native/download/sync_test_resources/.config.vsh.yaml b/target/native/download/sync_test_resources/.config.vsh.yaml index a0fea12680b..00597bdad52 100644 --- a/target/native/download/sync_test_resources/.config.vsh.yaml +++ b/target/native/download/sync_test_resources/.config.vsh.yaml @@ -165,6 +165,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/download/sync_test_resources" executable: "/home/runner/work/openpipeline/openpipeline/target/native/download/sync_test_resources/sync_test_resources" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/native/integrate/scarches/.config.vsh.yaml b/target/native/integrate/scarches/.config.vsh.yaml index c31484f2e09..5cd42ef7185 100644 --- a/target/native/integrate/scarches/.config.vsh.yaml +++ b/target/native/integrate/scarches/.config.vsh.yaml @@ -326,6 +326,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/integrate/scarches" executable: "/home/runner/work/openpipeline/openpipeline/target/native/integrate/scarches/scarches" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/native/integrate/totalvi/.config.vsh.yaml b/target/native/integrate/totalvi/.config.vsh.yaml index 7c60c8e98ad..54eeb4e7f9b 100644 --- a/target/native/integrate/totalvi/.config.vsh.yaml +++ b/target/native/integrate/totalvi/.config.vsh.yaml @@ -343,6 +343,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/integrate/totalvi" executable: "/home/runner/work/openpipeline/openpipeline/target/native/integrate/totalvi/totalvi" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/native/labels_transfer/knn/.config.vsh.yaml b/target/native/labels_transfer/knn/.config.vsh.yaml index 90020b27521..0b6913a03af 100644 --- a/target/native/labels_transfer/knn/.config.vsh.yaml +++ b/target/native/labels_transfer/knn/.config.vsh.yaml @@ -374,6 +374,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/labels_transfer/knn" executable: "/home/runner/work/openpipeline/openpipeline/target/native/labels_transfer/knn/knn" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/native/labels_transfer/xgboost/.config.vsh.yaml b/target/native/labels_transfer/xgboost/.config.vsh.yaml index 045915e405e..73880630f3e 100644 --- a/target/native/labels_transfer/xgboost/.config.vsh.yaml +++ b/target/native/labels_transfer/xgboost/.config.vsh.yaml @@ -589,6 +589,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/labels_transfer/xgboost" executable: "/home/runner/work/openpipeline/openpipeline/target/native/labels_transfer/xgboost/xgboost" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/native/metadata/add_id/.config.vsh.yaml b/target/native/metadata/add_id/.config.vsh.yaml index 76fe94b1936..5f6d540e16b 100644 --- a/target/native/metadata/add_id/.config.vsh.yaml +++ b/target/native/metadata/add_id/.config.vsh.yaml @@ -192,6 +192,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/metadata/add_id" executable: "/home/runner/work/openpipeline/openpipeline/target/native/metadata/add_id/add_id" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/native/metadata/grep_annotation_column/.config.vsh.yaml b/target/native/metadata/grep_annotation_column/.config.vsh.yaml index e6046c82751..68ce018021c 100644 --- a/target/native/metadata/grep_annotation_column/.config.vsh.yaml +++ b/target/native/metadata/grep_annotation_column/.config.vsh.yaml @@ -239,6 +239,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/metadata/grep_annotation_column" executable: "/home/runner/work/openpipeline/openpipeline/target/native/metadata/grep_annotation_column/grep_annotation_column" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/native/transform/scale/.config.vsh.yaml b/target/native/transform/scale/.config.vsh.yaml index 177fbcd66bc..fb77d3602b9 100644 --- a/target/native/transform/scale/.config.vsh.yaml +++ b/target/native/transform/scale/.config.vsh.yaml @@ -200,6 +200,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/transform/scale" executable: "/home/runner/work/openpipeline/openpipeline/target/native/transform/scale/scale" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/native/velocity/scvelo/.config.vsh.yaml b/target/native/velocity/scvelo/.config.vsh.yaml index b65b2cced7f..6675c39e806 100644 --- a/target/native/velocity/scvelo/.config.vsh.yaml +++ b/target/native/velocity/scvelo/.config.vsh.yaml @@ -271,6 +271,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/velocity/scvelo" executable: "/home/runner/work/openpipeline/openpipeline/target/native/velocity/scvelo/scvelo" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/native/velocity/velocyto/.config.vsh.yaml b/target/native/velocity/velocyto/.config.vsh.yaml index f1645b6b6db..c0ad44c1c4e 100644 --- a/target/native/velocity/velocyto/.config.vsh.yaml +++ b/target/native/velocity/velocyto/.config.vsh.yaml @@ -220,6 +220,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/velocity/velocyto" executable: "/home/runner/work/openpipeline/openpipeline/target/native/velocity/velocyto/velocyto" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/annotate/popv/.config.vsh.yaml b/target/nextflow/annotate/popv/.config.vsh.yaml index 17d55cff20e..7518edac8f4 100644 --- a/target/nextflow/annotate/popv/.config.vsh.yaml +++ b/target/nextflow/annotate/popv/.config.vsh.yaml @@ -341,6 +341,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/annotate/popv" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/annotate/popv/popv" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/annotate/popv/main.nf b/target/nextflow/annotate/popv/main.nf index c800f3dd90e..f950802b925 100644 --- a/target/nextflow/annotate/popv/main.nf +++ b/target/nextflow/annotate/popv/main.nf @@ -459,9 +459,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/annotate/popv", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/cluster/leiden/.config.vsh.yaml b/target/nextflow/cluster/leiden/.config.vsh.yaml index 99671f06bb0..d25c28179c2 100644 --- a/target/nextflow/cluster/leiden/.config.vsh.yaml +++ b/target/nextflow/cluster/leiden/.config.vsh.yaml @@ -214,6 +214,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/cluster/leiden" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/cluster/leiden/leiden" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/cluster/leiden/main.nf b/target/nextflow/cluster/leiden/main.nf index 2e74e4efcea..cdc45b85237 100644 --- a/target/nextflow/cluster/leiden/main.nf +++ b/target/nextflow/cluster/leiden/main.nf @@ -285,9 +285,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/cluster/leiden", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/compression/compress_h5mu/.config.vsh.yaml b/target/nextflow/compression/compress_h5mu/.config.vsh.yaml index 4e40dc3a37d..925a68624c3 100644 --- a/target/nextflow/compression/compress_h5mu/.config.vsh.yaml +++ b/target/nextflow/compression/compress_h5mu/.config.vsh.yaml @@ -162,6 +162,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/compression/compress_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/compression/compress_h5mu/compress_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/compression/compress_h5mu/main.nf b/target/nextflow/compression/compress_h5mu/main.nf index fcfcdc1371e..8254d02b797 100644 --- a/target/nextflow/compression/compress_h5mu/main.nf +++ b/target/nextflow/compression/compress_h5mu/main.nf @@ -241,9 +241,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/compression/compress_h5mu", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/convert/from_10xh5_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_10xh5_to_h5mu/.config.vsh.yaml index d8b82c1c141..b951eb52bcc 100644 --- a/target/nextflow/convert/from_10xh5_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_10xh5_to_h5mu/.config.vsh.yaml @@ -267,6 +267,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_10xh5_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/convert/from_10xh5_to_h5mu/main.nf b/target/nextflow/convert/from_10xh5_to_h5mu/main.nf index 8e54ab7d43f..7cbe56f7886 100644 --- a/target/nextflow/convert/from_10xh5_to_h5mu/main.nf +++ b/target/nextflow/convert/from_10xh5_to_h5mu/main.nf @@ -394,9 +394,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_10xh5_to_h5mu", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/convert/from_10xmtx_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_10xmtx_to_h5mu/.config.vsh.yaml index 662cc1704b9..86116d80b03 100644 --- a/target/nextflow/convert/from_10xmtx_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_10xmtx_to_h5mu/.config.vsh.yaml @@ -161,6 +161,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_10xmtx_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/convert/from_10xmtx_to_h5mu/main.nf b/target/nextflow/convert/from_10xmtx_to_h5mu/main.nf index 3de1d3399c2..523ad8fcdf0 100644 --- a/target/nextflow/convert/from_10xmtx_to_h5mu/main.nf +++ b/target/nextflow/convert/from_10xmtx_to_h5mu/main.nf @@ -238,9 +238,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_10xmtx_to_h5mu", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml index 288c029ba7d..05904731e0e 100644 --- a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml +++ b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml @@ -154,6 +154,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf index 45121186e08..2b89e2d05fb 100644 --- a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf +++ b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf @@ -222,9 +222,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/convert/from_bdrhap_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_bdrhap_to_h5mu/.config.vsh.yaml index 34afc975fe7..2eb7adf87f1 100644 --- a/target/nextflow/convert/from_bdrhap_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_bdrhap_to_h5mu/.config.vsh.yaml @@ -176,6 +176,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_bdrhap_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/convert/from_bdrhap_to_h5mu/main.nf b/target/nextflow/convert/from_bdrhap_to_h5mu/main.nf index c6aec766877..18e88385f54 100644 --- a/target/nextflow/convert/from_bdrhap_to_h5mu/main.nf +++ b/target/nextflow/convert/from_bdrhap_to_h5mu/main.nf @@ -261,9 +261,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_bdrhap_to_h5mu", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml index 85f7382b0a6..3637e858568 100644 --- a/target/nextflow/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml @@ -185,6 +185,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_cellranger_multi_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf b/target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf index 3fa5d6e732e..51e2c6b7e1c 100644 --- a/target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf +++ b/target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf @@ -263,9 +263,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_cellranger_multi_to_h5mu", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/convert/from_h5ad_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_h5ad_to_h5mu/.config.vsh.yaml index a4f851e6ce1..debbdefa32d 100644 --- a/target/nextflow/convert/from_h5ad_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_h5ad_to_h5mu/.config.vsh.yaml @@ -172,6 +172,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_h5ad_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/convert/from_h5ad_to_h5mu/main.nf b/target/nextflow/convert/from_h5ad_to_h5mu/main.nf index 808b0be75d5..db66231f3de 100644 --- a/target/nextflow/convert/from_h5ad_to_h5mu/main.nf +++ b/target/nextflow/convert/from_h5ad_to_h5mu/main.nf @@ -253,9 +253,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_h5ad_to_h5mu", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/convert/from_h5mu_to_h5ad/.config.vsh.yaml b/target/nextflow/convert/from_h5mu_to_h5ad/.config.vsh.yaml index 9f4f3db5ef6..4625071bb70 100644 --- a/target/nextflow/convert/from_h5mu_to_h5ad/.config.vsh.yaml +++ b/target/nextflow/convert/from_h5mu_to_h5ad/.config.vsh.yaml @@ -177,6 +177,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_h5mu_to_h5ad" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/convert/from_h5mu_to_h5ad/main.nf b/target/nextflow/convert/from_h5mu_to_h5ad/main.nf index 968c64ce822..f96ba6d0319 100644 --- a/target/nextflow/convert/from_h5mu_to_h5ad/main.nf +++ b/target/nextflow/convert/from_h5mu_to_h5ad/main.nf @@ -260,9 +260,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_h5mu_to_h5ad", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/convert/velocyto_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/velocyto_to_h5mu/.config.vsh.yaml index 03d8c32c6ac..a86e9fae886 100644 --- a/target/nextflow/convert/velocyto_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/velocyto_to_h5mu/.config.vsh.yaml @@ -250,6 +250,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/velocyto_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/velocyto_to_h5mu/velocyto_to_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/convert/velocyto_to_h5mu/main.nf b/target/nextflow/convert/velocyto_to_h5mu/main.nf index 0bf4739d2db..bf693750051 100644 --- a/target/nextflow/convert/velocyto_to_h5mu/main.nf +++ b/target/nextflow/convert/velocyto_to_h5mu/main.nf @@ -357,9 +357,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/velocyto_to_h5mu", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/correction/cellbender_remove_background/.config.vsh.yaml b/target/nextflow/correction/cellbender_remove_background/.config.vsh.yaml index c807a86be9d..e07121119b5 100644 --- a/target/nextflow/correction/cellbender_remove_background/.config.vsh.yaml +++ b/target/nextflow/correction/cellbender_remove_background/.config.vsh.yaml @@ -632,6 +632,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/correction/cellbender_remove_background" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/correction/cellbender_remove_background/cellbender_remove_background" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/correction/cellbender_remove_background/main.nf b/target/nextflow/correction/cellbender_remove_background/main.nf index 6fe8e3abcc2..7fea2cc19c3 100644 --- a/target/nextflow/correction/cellbender_remove_background/main.nf +++ b/target/nextflow/correction/cellbender_remove_background/main.nf @@ -706,9 +706,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/correction/cellbender_remove_background", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/correction/cellbender_remove_background_v0_2/.config.vsh.yaml b/target/nextflow/correction/cellbender_remove_background_v0_2/.config.vsh.yaml index f302e49c060..798f58bacca 100644 --- a/target/nextflow/correction/cellbender_remove_background_v0_2/.config.vsh.yaml +++ b/target/nextflow/correction/cellbender_remove_background_v0_2/.config.vsh.yaml @@ -401,6 +401,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/correction/cellbender_remove_background_v0_2" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/correction/cellbender_remove_background_v0_2/cellbender_remove_background_v0_2" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/correction/cellbender_remove_background_v0_2/main.nf b/target/nextflow/correction/cellbender_remove_background_v0_2/main.nf index c832367581c..7ed3e19518b 100644 --- a/target/nextflow/correction/cellbender_remove_background_v0_2/main.nf +++ b/target/nextflow/correction/cellbender_remove_background_v0_2/main.nf @@ -492,9 +492,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/correction/cellbender_remove_background_v0_2", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/dataflow/concat/.config.vsh.yaml b/target/nextflow/dataflow/concat/.config.vsh.yaml index 282b0f1af76..3a98bf31ed3 100644 --- a/target/nextflow/dataflow/concat/.config.vsh.yaml +++ b/target/nextflow/dataflow/concat/.config.vsh.yaml @@ -217,6 +217,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/concat" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/concat/concat" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/dataflow/concat/main.nf b/target/nextflow/dataflow/concat/main.nf index b417ce315bf..dfb027d5c2a 100644 --- a/target/nextflow/dataflow/concat/main.nf +++ b/target/nextflow/dataflow/concat/main.nf @@ -297,9 +297,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/concat", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) @@ -441,20 +441,19 @@ def any_row_contains_duplicate_values(n_processes: int, frame: pd.DataFrame) -> is_duplicated = pool.map(nunique, iter(numpy_array)) return any(is_duplicated) -def concatenate_matrices(n_processes: int, input_ids: tuple[str], matrices: Iterable[pd.DataFrame], align_to: pd.Index | None) \\\\ +def concatenate_matrices(n_processes: int, matrices: dict[str, pd.DataFrame], align_to: pd.Index | None) \\\\ -> tuple[dict[str, pd.DataFrame], pd.DataFrame | None, dict[str, pd.core.dtypes.dtypes.Dtype]]: """ Merge matrices by combining columns that have the same name. Columns that contain conflicting values (e.i. the columns have different values), are not merged, but instead moved to a new dataframe. """ - column_names = set(column_name for var in matrices for column_name in var) + column_names = set(column_name for var in matrices.values() for column_name in var) logger.debug('Trying to concatenate columns: %s.', ",".join(column_names)) if not column_names: return {}, pd.DataFrame(index=align_to) conflicts, concatenated_matrix = \\\\ split_conflicts_and_concatenated_columns(n_processes, - input_ids, matrices, column_names, align_to) @@ -471,8 +470,7 @@ def get_first_non_na_value_vector(df): return pd.Series(numpy_arr.ravel()[flat_index], index=df.index, name=df.columns[0]) def split_conflicts_and_concatenated_columns(n_processes: int, - input_ids: tuple[str], - matrices: Iterable[pd.DataFrame], + matrices: dict[str, pd.DataFrame], column_names: Iterable[str], align_to: pd.Index | None = None) -> \\\\ tuple[dict[str, pd.DataFrame], pd.DataFrame]: @@ -486,14 +484,17 @@ def split_conflicts_and_concatenated_columns(n_processes: int, conflicts = {} concatenated_matrix = [] for column_name in column_names: - columns = [var[column_name] for var in matrices if column_name in var] + columns = {input_id: var[column_name] + for input_id, var in matrices.items() + if column_name in var} assert columns, "Some columns should have been found." - concatenated_columns = pd.concat(columns, axis=1, join="outer", sort=False) + concatenated_columns = pd.concat(columns.values(), axis=1, + join="outer", sort=False) if any_row_contains_duplicate_values(n_processes, concatenated_columns): - concatenated_columns.columns = input_ids + concatenated_columns.columns = columns.keys() # Use the sample id as column name if align_to is not None: concatenated_columns = concatenated_columns.reindex(align_to, copy=False) - conflicts[f'conflict_{column_name}'] = concatenated_columns + conflicts[f'conflict_{column_name}'] = concatenated_columns else: unique_values = get_first_non_na_value_vector(concatenated_columns) concatenated_matrix.append(unique_values) @@ -527,7 +528,7 @@ def cast_to_writeable_dtype(result: pd.DataFrame) -> pd.DataFrame: result[obj_col] = result[obj_col].where(result[obj_col].isna(), result[obj_col].astype(str)).astype('category') return result -def split_conflicts_modalities(n_processes: int, input_ids: tuple[str], samples: Iterable[anndata.AnnData], output: anndata.AnnData) \\\\ +def split_conflicts_modalities(n_processes: int, samples: dict[str, anndata.AnnData], output: anndata.AnnData) \\\\ -> anndata.AnnData: """ Merge .var and .obs matrices of the anndata objects. Columns are merged @@ -537,10 +538,10 @@ def split_conflicts_modalities(n_processes: int, input_ids: tuple[str], samples: """ matrices_to_parse = ("var", "obs") for matrix_name in matrices_to_parse: - matrices = [getattr(sample, matrix_name) for sample in samples] + matrices = {sample_id: getattr(sample, matrix_name) for sample_id, sample in samples.items()} output_index = getattr(output, matrix_name).index align_to = output_index if matrix_name == "var" else None - conflicts, concatenated_matrix = concatenate_matrices(n_processes, input_ids, matrices, align_to) + conflicts, concatenated_matrix = concatenate_matrices(n_processes, matrices, align_to) if concatenated_matrix.empty: concatenated_matrix.index = output_index # Write the conflicts to the output @@ -561,20 +562,20 @@ def concatenate_modality(n_processes: int, mod: str, input_files: Iterable[str | } other_axis_mode_to_apply = concat_modes.get(other_axis_mode, other_axis_mode) - mod_data = [] - for input_file in input_files: + mod_data = {} + for input_id, input_file in zip(input_ids, input_files): try: - mod_data.append(mu.read_h5ad(input_file, mod=mod)) + mod_data[input_id] = mu.read_h5ad(input_file, mod=mod) except KeyError as e: # Modality does not exist for this sample, skip it if f"Unable to open object '{mod}' doesn't exist" not in str(e): raise e pass - check_observations_unique(mod_data) + check_observations_unique(mod_data.values()) - concatenated_data = anndata.concat(mod_data, join='outer', merge=other_axis_mode_to_apply) + concatenated_data = anndata.concat(mod_data.values(), join='outer', merge=other_axis_mode_to_apply) if other_axis_mode == "move": - concatenated_data = split_conflicts_modalities(n_processes, input_ids, mod_data, concatenated_data) + concatenated_data = split_conflicts_modalities(n_processes, mod_data, concatenated_data) return concatenated_data diff --git a/target/nextflow/dataflow/merge/.config.vsh.yaml b/target/nextflow/dataflow/merge/.config.vsh.yaml index 54f4acaae15..71715a30356 100644 --- a/target/nextflow/dataflow/merge/.config.vsh.yaml +++ b/target/nextflow/dataflow/merge/.config.vsh.yaml @@ -170,6 +170,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/merge" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/merge/merge" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/dataflow/merge/main.nf b/target/nextflow/dataflow/merge/main.nf index 852a86de49f..50b5dc02cef 100644 --- a/target/nextflow/dataflow/merge/main.nf +++ b/target/nextflow/dataflow/merge/main.nf @@ -253,9 +253,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/merge", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/dataflow/split_modalities/.config.vsh.yaml b/target/nextflow/dataflow/split_modalities/.config.vsh.yaml index 5bd74302865..36fd7afc059 100644 --- a/target/nextflow/dataflow/split_modalities/.config.vsh.yaml +++ b/target/nextflow/dataflow/split_modalities/.config.vsh.yaml @@ -209,6 +209,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/split_modalities" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/split_modalities/split_modalities" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/dataflow/split_modalities/main.nf b/target/nextflow/dataflow/split_modalities/main.nf index c13605bddd0..d64dd97a720 100644 --- a/target/nextflow/dataflow/split_modalities/main.nf +++ b/target/nextflow/dataflow/split_modalities/main.nf @@ -303,9 +303,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/split_modalities", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/demux/bcl2fastq/.config.vsh.yaml b/target/nextflow/demux/bcl2fastq/.config.vsh.yaml index bbb2f3fd1aa..4b57441e50f 100644 --- a/target/nextflow/demux/bcl2fastq/.config.vsh.yaml +++ b/target/nextflow/demux/bcl2fastq/.config.vsh.yaml @@ -164,6 +164,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/bcl2fastq" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/bcl2fastq/bcl2fastq" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/demux/bcl2fastq/main.nf b/target/nextflow/demux/bcl2fastq/main.nf index 6c69d8680cb..99d76399634 100644 --- a/target/nextflow/demux/bcl2fastq/main.nf +++ b/target/nextflow/demux/bcl2fastq/main.nf @@ -232,9 +232,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/bcl2fastq", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/demux/bcl_convert/.config.vsh.yaml b/target/nextflow/demux/bcl_convert/.config.vsh.yaml index 55601657969..976471a7e63 100644 --- a/target/nextflow/demux/bcl_convert/.config.vsh.yaml +++ b/target/nextflow/demux/bcl_convert/.config.vsh.yaml @@ -184,6 +184,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/bcl_convert" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/bcl_convert/bcl_convert" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/demux/bcl_convert/main.nf b/target/nextflow/demux/bcl_convert/main.nf index ed7db1057e4..423ef5522a9 100644 --- a/target/nextflow/demux/bcl_convert/main.nf +++ b/target/nextflow/demux/bcl_convert/main.nf @@ -260,9 +260,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/bcl_convert", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/demux/cellranger_mkfastq/.config.vsh.yaml b/target/nextflow/demux/cellranger_mkfastq/.config.vsh.yaml index daa2283b8f5..fb11e2898b1 100644 --- a/target/nextflow/demux/cellranger_mkfastq/.config.vsh.yaml +++ b/target/nextflow/demux/cellranger_mkfastq/.config.vsh.yaml @@ -202,6 +202,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/cellranger_mkfastq" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/cellranger_mkfastq/cellranger_mkfastq" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/demux/cellranger_mkfastq/main.nf b/target/nextflow/demux/cellranger_mkfastq/main.nf index f57df159748..e1de17d2434 100644 --- a/target/nextflow/demux/cellranger_mkfastq/main.nf +++ b/target/nextflow/demux/cellranger_mkfastq/main.nf @@ -298,9 +298,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/cellranger_mkfastq", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/dimred/pca/.config.vsh.yaml b/target/nextflow/dimred/pca/.config.vsh.yaml index 5fb127ec5c4..37ef15ac31d 100644 --- a/target/nextflow/dimred/pca/.config.vsh.yaml +++ b/target/nextflow/dimred/pca/.config.vsh.yaml @@ -248,6 +248,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/pca" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/pca/pca" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/dimred/pca/main.nf b/target/nextflow/dimred/pca/main.nf index 86f49255578..4a6f2229c27 100644 --- a/target/nextflow/dimred/pca/main.nf +++ b/target/nextflow/dimred/pca/main.nf @@ -337,9 +337,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/pca", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/dimred/umap/.config.vsh.yaml b/target/nextflow/dimred/umap/.config.vsh.yaml index f49c809ba97..ea4349c006f 100644 --- a/target/nextflow/dimred/umap/.config.vsh.yaml +++ b/target/nextflow/dimred/umap/.config.vsh.yaml @@ -307,6 +307,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/umap" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/umap/umap" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/dimred/umap/main.nf b/target/nextflow/dimred/umap/main.nf index 01de7b7c788..6938628bc36 100644 --- a/target/nextflow/dimred/umap/main.nf +++ b/target/nextflow/dimred/umap/main.nf @@ -394,9 +394,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/umap", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/download/download_file/.config.vsh.yaml b/target/nextflow/download/download_file/.config.vsh.yaml index ca1e4e844f4..da764f92807 100644 --- a/target/nextflow/download/download_file/.config.vsh.yaml +++ b/target/nextflow/download/download_file/.config.vsh.yaml @@ -133,6 +133,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/download/download_file" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/download/download_file/download_file" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/download/download_file/main.nf b/target/nextflow/download/download_file/main.nf index 24dcbcedaa3..4bb1fd5ef59 100644 --- a/target/nextflow/download/download_file/main.nf +++ b/target/nextflow/download/download_file/main.nf @@ -192,9 +192,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/download/download_file", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/download/sync_test_resources/.config.vsh.yaml b/target/nextflow/download/sync_test_resources/.config.vsh.yaml index 3787cb76f50..059e4e8040c 100644 --- a/target/nextflow/download/sync_test_resources/.config.vsh.yaml +++ b/target/nextflow/download/sync_test_resources/.config.vsh.yaml @@ -165,6 +165,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/download/sync_test_resources" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/download/sync_test_resources/sync_test_resources" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/download/sync_test_resources/main.nf b/target/nextflow/download/sync_test_resources/main.nf index b54907feeaa..11ec7f69c86 100644 --- a/target/nextflow/download/sync_test_resources/main.nf +++ b/target/nextflow/download/sync_test_resources/main.nf @@ -231,9 +231,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/download/sync_test_resources", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/files/make_params/.config.vsh.yaml b/target/nextflow/files/make_params/.config.vsh.yaml index 149c516ec1c..dd4d69a25d9 100644 --- a/target/nextflow/files/make_params/.config.vsh.yaml +++ b/target/nextflow/files/make_params/.config.vsh.yaml @@ -215,6 +215,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/files/make_params" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/files/make_params/make_params" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/files/make_params/main.nf b/target/nextflow/files/make_params/main.nf index 776c1e797b7..a7bb9012e26 100644 --- a/target/nextflow/files/make_params/main.nf +++ b/target/nextflow/files/make_params/main.nf @@ -298,9 +298,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/files/make_params", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/filter/delimit_fraction/.config.vsh.yaml b/target/nextflow/filter/delimit_fraction/.config.vsh.yaml index 1341631171f..2e6fea8bf10 100644 --- a/target/nextflow/filter/delimit_fraction/.config.vsh.yaml +++ b/target/nextflow/filter/delimit_fraction/.config.vsh.yaml @@ -236,6 +236,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/delimit_fraction" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/delimit_fraction/delimit_fraction" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/filter/delimit_fraction/main.nf b/target/nextflow/filter/delimit_fraction/main.nf index 290a86bea8b..6d98952a370 100644 --- a/target/nextflow/filter/delimit_fraction/main.nf +++ b/target/nextflow/filter/delimit_fraction/main.nf @@ -330,9 +330,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/delimit_fraction", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/filter/do_filter/.config.vsh.yaml b/target/nextflow/filter/do_filter/.config.vsh.yaml index 5afef5f6584..c8212d38c48 100644 --- a/target/nextflow/filter/do_filter/.config.vsh.yaml +++ b/target/nextflow/filter/do_filter/.config.vsh.yaml @@ -197,6 +197,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/do_filter" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/do_filter/do_filter" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/filter/do_filter/main.nf b/target/nextflow/filter/do_filter/main.nf index a2ba27dc399..74c3d36b1a4 100644 --- a/target/nextflow/filter/do_filter/main.nf +++ b/target/nextflow/filter/do_filter/main.nf @@ -281,9 +281,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/do_filter", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/filter/filter_with_counts/.config.vsh.yaml b/target/nextflow/filter/filter_with_counts/.config.vsh.yaml index be9769bf24f..55373a7f6b4 100644 --- a/target/nextflow/filter/filter_with_counts/.config.vsh.yaml +++ b/target/nextflow/filter/filter_with_counts/.config.vsh.yaml @@ -290,6 +290,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_counts" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_counts/filter_with_counts" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/filter/filter_with_counts/main.nf b/target/nextflow/filter/filter_with_counts/main.nf index ca931b46829..b4caa05f754 100644 --- a/target/nextflow/filter/filter_with_counts/main.nf +++ b/target/nextflow/filter/filter_with_counts/main.nf @@ -402,9 +402,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_counts", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/filter/filter_with_hvg/.config.vsh.yaml b/target/nextflow/filter/filter_with_hvg/.config.vsh.yaml index 7bcdf6c5a80..b0b39549609 100644 --- a/target/nextflow/filter/filter_with_hvg/.config.vsh.yaml +++ b/target/nextflow/filter/filter_with_hvg/.config.vsh.yaml @@ -347,6 +347,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_hvg" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_hvg/filter_with_hvg" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/filter/filter_with_hvg/main.nf b/target/nextflow/filter/filter_with_hvg/main.nf index d53aa3178c6..feafe9151b2 100644 --- a/target/nextflow/filter/filter_with_hvg/main.nf +++ b/target/nextflow/filter/filter_with_hvg/main.nf @@ -428,9 +428,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_hvg", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/filter/filter_with_scrublet/.config.vsh.yaml b/target/nextflow/filter/filter_with_scrublet/.config.vsh.yaml index 451a1c122cd..1d6bb387537 100644 --- a/target/nextflow/filter/filter_with_scrublet/.config.vsh.yaml +++ b/target/nextflow/filter/filter_with_scrublet/.config.vsh.yaml @@ -299,6 +299,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_scrublet" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_scrublet/filter_with_scrublet" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/filter/filter_with_scrublet/main.nf b/target/nextflow/filter/filter_with_scrublet/main.nf index 0a943278600..99f3b551e8d 100644 --- a/target/nextflow/filter/filter_with_scrublet/main.nf +++ b/target/nextflow/filter/filter_with_scrublet/main.nf @@ -389,9 +389,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_scrublet", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/filter/remove_modality/.config.vsh.yaml b/target/nextflow/filter/remove_modality/.config.vsh.yaml index 8fcbb50725c..98d5c843268 100644 --- a/target/nextflow/filter/remove_modality/.config.vsh.yaml +++ b/target/nextflow/filter/remove_modality/.config.vsh.yaml @@ -166,6 +166,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/remove_modality" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/remove_modality/remove_modality" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/filter/remove_modality/main.nf b/target/nextflow/filter/remove_modality/main.nf index b15a8151227..1d98b535470 100644 --- a/target/nextflow/filter/remove_modality/main.nf +++ b/target/nextflow/filter/remove_modality/main.nf @@ -241,9 +241,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/remove_modality", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/filter/subset_h5mu/.config.vsh.yaml b/target/nextflow/filter/subset_h5mu/.config.vsh.yaml index f12b48c65f6..cdfe7d13abb 100644 --- a/target/nextflow/filter/subset_h5mu/.config.vsh.yaml +++ b/target/nextflow/filter/subset_h5mu/.config.vsh.yaml @@ -182,6 +182,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/subset_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/subset_h5mu/subset_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/filter/subset_h5mu/main.nf b/target/nextflow/filter/subset_h5mu/main.nf index 18feae87388..0def3d04067 100644 --- a/target/nextflow/filter/subset_h5mu/main.nf +++ b/target/nextflow/filter/subset_h5mu/main.nf @@ -262,9 +262,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/subset_h5mu", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/integrate/harmonypy/.config.vsh.yaml b/target/nextflow/integrate/harmonypy/.config.vsh.yaml index 30baf328a2d..14fe5ee1c33 100644 --- a/target/nextflow/integrate/harmonypy/.config.vsh.yaml +++ b/target/nextflow/integrate/harmonypy/.config.vsh.yaml @@ -235,6 +235,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/harmonypy" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/harmonypy/harmonypy" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/integrate/harmonypy/main.nf b/target/nextflow/integrate/harmonypy/main.nf index c0c1a3752c6..8fd0689c681 100644 --- a/target/nextflow/integrate/harmonypy/main.nf +++ b/target/nextflow/integrate/harmonypy/main.nf @@ -327,9 +327,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/harmonypy", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/integrate/scanorama/.config.vsh.yaml b/target/nextflow/integrate/scanorama/.config.vsh.yaml index 0fb2fa6ac25..556f08c99b6 100644 --- a/target/nextflow/integrate/scanorama/.config.vsh.yaml +++ b/target/nextflow/integrate/scanorama/.config.vsh.yaml @@ -278,6 +278,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scanorama" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scanorama/scanorama" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/integrate/scanorama/main.nf b/target/nextflow/integrate/scanorama/main.nf index ce3457804f0..ba8863ed99a 100644 --- a/target/nextflow/integrate/scanorama/main.nf +++ b/target/nextflow/integrate/scanorama/main.nf @@ -376,9 +376,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scanorama", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/integrate/scarches/.config.vsh.yaml b/target/nextflow/integrate/scarches/.config.vsh.yaml index 4b6be3dc039..dd77332a214 100644 --- a/target/nextflow/integrate/scarches/.config.vsh.yaml +++ b/target/nextflow/integrate/scarches/.config.vsh.yaml @@ -326,6 +326,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scarches" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scarches/scarches" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/integrate/scarches/main.nf b/target/nextflow/integrate/scarches/main.nf index 0e83eec6e98..4b928080a66 100644 --- a/target/nextflow/integrate/scarches/main.nf +++ b/target/nextflow/integrate/scarches/main.nf @@ -433,9 +433,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scarches", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/integrate/scvi/.config.vsh.yaml b/target/nextflow/integrate/scvi/.config.vsh.yaml index 2cb16d57379..b0336fa962b 100644 --- a/target/nextflow/integrate/scvi/.config.vsh.yaml +++ b/target/nextflow/integrate/scvi/.config.vsh.yaml @@ -586,6 +586,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scvi" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scvi/scvi" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/integrate/scvi/main.nf b/target/nextflow/integrate/scvi/main.nf index e233571e87b..be868125220 100644 --- a/target/nextflow/integrate/scvi/main.nf +++ b/target/nextflow/integrate/scvi/main.nf @@ -738,9 +738,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scvi", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/integrate/totalvi/.config.vsh.yaml b/target/nextflow/integrate/totalvi/.config.vsh.yaml index c3f68db8875..b8dbc1cb07b 100644 --- a/target/nextflow/integrate/totalvi/.config.vsh.yaml +++ b/target/nextflow/integrate/totalvi/.config.vsh.yaml @@ -343,6 +343,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/totalvi" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/totalvi/totalvi" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/integrate/totalvi/main.nf b/target/nextflow/integrate/totalvi/main.nf index 6fc415dd93b..df2d508e7ee 100644 --- a/target/nextflow/integrate/totalvi/main.nf +++ b/target/nextflow/integrate/totalvi/main.nf @@ -453,9 +453,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/totalvi", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/interpret/lianapy/.config.vsh.yaml b/target/nextflow/interpret/lianapy/.config.vsh.yaml index 0a300f078b8..1fe32159ae0 100644 --- a/target/nextflow/interpret/lianapy/.config.vsh.yaml +++ b/target/nextflow/interpret/lianapy/.config.vsh.yaml @@ -308,6 +308,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/interpret/lianapy" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/interpret/lianapy/lianapy" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/interpret/lianapy/main.nf b/target/nextflow/interpret/lianapy/main.nf index 725e43e5f43..32a8fe671ae 100644 --- a/target/nextflow/interpret/lianapy/main.nf +++ b/target/nextflow/interpret/lianapy/main.nf @@ -404,9 +404,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/interpret/lianapy", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/labels_transfer/knn/.config.vsh.yaml b/target/nextflow/labels_transfer/knn/.config.vsh.yaml index 9c1a8861997..8f099934250 100644 --- a/target/nextflow/labels_transfer/knn/.config.vsh.yaml +++ b/target/nextflow/labels_transfer/knn/.config.vsh.yaml @@ -374,6 +374,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/labels_transfer/knn" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/labels_transfer/knn/knn" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/labels_transfer/knn/main.nf b/target/nextflow/labels_transfer/knn/main.nf index 4a532b52c94..c65164cb08a 100644 --- a/target/nextflow/labels_transfer/knn/main.nf +++ b/target/nextflow/labels_transfer/knn/main.nf @@ -500,9 +500,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/labels_transfer/knn", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/labels_transfer/xgboost/.config.vsh.yaml b/target/nextflow/labels_transfer/xgboost/.config.vsh.yaml index 40971ff3182..e2887b6c124 100644 --- a/target/nextflow/labels_transfer/xgboost/.config.vsh.yaml +++ b/target/nextflow/labels_transfer/xgboost/.config.vsh.yaml @@ -589,6 +589,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/labels_transfer/xgboost" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/labels_transfer/xgboost/xgboost" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/labels_transfer/xgboost/main.nf b/target/nextflow/labels_transfer/xgboost/main.nf index e55964440c8..161cfb54a5e 100644 --- a/target/nextflow/labels_transfer/xgboost/main.nf +++ b/target/nextflow/labels_transfer/xgboost/main.nf @@ -736,9 +736,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/labels_transfer/xgboost", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/mapping/bd_rhapsody/.config.vsh.yaml b/target/nextflow/mapping/bd_rhapsody/.config.vsh.yaml index dbd212508a5..72f3da797a9 100644 --- a/target/nextflow/mapping/bd_rhapsody/.config.vsh.yaml +++ b/target/nextflow/mapping/bd_rhapsody/.config.vsh.yaml @@ -412,6 +412,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/bd_rhapsody" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/bd_rhapsody/bd_rhapsody" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/mapping/bd_rhapsody/main.nf b/target/nextflow/mapping/bd_rhapsody/main.nf index 61375d54b58..4698ab4afbd 100644 --- a/target/nextflow/mapping/bd_rhapsody/main.nf +++ b/target/nextflow/mapping/bd_rhapsody/main.nf @@ -532,9 +532,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/bd_rhapsody", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/mapping/cellranger_count/.config.vsh.yaml b/target/nextflow/mapping/cellranger_count/.config.vsh.yaml index a27c3b5a76a..b754fc36012 100644 --- a/target/nextflow/mapping/cellranger_count/.config.vsh.yaml +++ b/target/nextflow/mapping/cellranger_count/.config.vsh.yaml @@ -261,6 +261,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_count" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_count/cellranger_count" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/mapping/cellranger_count/main.nf b/target/nextflow/mapping/cellranger_count/main.nf index e33ce18933c..56b530e78e1 100644 --- a/target/nextflow/mapping/cellranger_count/main.nf +++ b/target/nextflow/mapping/cellranger_count/main.nf @@ -363,9 +363,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_count", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/mapping/cellranger_count_split/.config.vsh.yaml b/target/nextflow/mapping/cellranger_count_split/.config.vsh.yaml index cf56e5f93eb..fac2388e7eb 100644 --- a/target/nextflow/mapping/cellranger_count_split/.config.vsh.yaml +++ b/target/nextflow/mapping/cellranger_count_split/.config.vsh.yaml @@ -213,6 +213,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_count_split" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_count_split/cellranger_count_split" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/mapping/cellranger_count_split/main.nf b/target/nextflow/mapping/cellranger_count_split/main.nf index dc0b3729b77..26ff26016ed 100644 --- a/target/nextflow/mapping/cellranger_count_split/main.nf +++ b/target/nextflow/mapping/cellranger_count_split/main.nf @@ -301,9 +301,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_count_split", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/mapping/cellranger_multi/.config.vsh.yaml b/target/nextflow/mapping/cellranger_multi/.config.vsh.yaml index 76dab6af930..7e9ca75621a 100644 --- a/target/nextflow/mapping/cellranger_multi/.config.vsh.yaml +++ b/target/nextflow/mapping/cellranger_multi/.config.vsh.yaml @@ -418,6 +418,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_multi" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_multi/cellranger_multi" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/mapping/cellranger_multi/main.nf b/target/nextflow/mapping/cellranger_multi/main.nf index 523b7179d4d..3ba8bbecac8 100644 --- a/target/nextflow/mapping/cellranger_multi/main.nf +++ b/target/nextflow/mapping/cellranger_multi/main.nf @@ -545,9 +545,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_multi", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/mapping/htseq_count/.config.vsh.yaml b/target/nextflow/mapping/htseq_count/.config.vsh.yaml index 9bc3a405451..ced73cd1c29 100644 --- a/target/nextflow/mapping/htseq_count/.config.vsh.yaml +++ b/target/nextflow/mapping/htseq_count/.config.vsh.yaml @@ -413,6 +413,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/htseq_count" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/htseq_count/htseq_count" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/mapping/htseq_count/main.nf b/target/nextflow/mapping/htseq_count/main.nf index 28844768437..6877e869652 100644 --- a/target/nextflow/mapping/htseq_count/main.nf +++ b/target/nextflow/mapping/htseq_count/main.nf @@ -553,9 +553,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/htseq_count", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/mapping/htseq_count_to_h5mu/.config.vsh.yaml b/target/nextflow/mapping/htseq_count_to_h5mu/.config.vsh.yaml index 199bfb27346..98e9f4afa34 100644 --- a/target/nextflow/mapping/htseq_count_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/mapping/htseq_count_to_h5mu/.config.vsh.yaml @@ -204,6 +204,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/htseq_count_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/mapping/htseq_count_to_h5mu/main.nf b/target/nextflow/mapping/htseq_count_to_h5mu/main.nf index bda0e00afef..7e64b6f4658 100644 --- a/target/nextflow/mapping/htseq_count_to_h5mu/main.nf +++ b/target/nextflow/mapping/htseq_count_to_h5mu/main.nf @@ -298,9 +298,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/htseq_count_to_h5mu", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/mapping/multi_star/.config.vsh.yaml b/target/nextflow/mapping/multi_star/.config.vsh.yaml index b0dc44a8624..e891bb4bbb9 100644 --- a/target/nextflow/mapping/multi_star/.config.vsh.yaml +++ b/target/nextflow/mapping/multi_star/.config.vsh.yaml @@ -3075,6 +3075,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/multi_star" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/multi_star/multi_star" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/mapping/multi_star/main.nf b/target/nextflow/mapping/multi_star/main.nf index 5e7fc443464..b40985a9bf4 100644 --- a/target/nextflow/mapping/multi_star/main.nf +++ b/target/nextflow/mapping/multi_star/main.nf @@ -3595,9 +3595,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/multi_star", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/mapping/multi_star_to_h5mu/.config.vsh.yaml b/target/nextflow/mapping/multi_star_to_h5mu/.config.vsh.yaml index a9a0e04b493..ba85db61dc0 100644 --- a/target/nextflow/mapping/multi_star_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/mapping/multi_star_to_h5mu/.config.vsh.yaml @@ -174,6 +174,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/multi_star_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/multi_star_to_h5mu/multi_star_to_h5mu" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/mapping/multi_star_to_h5mu/main.nf b/target/nextflow/mapping/multi_star_to_h5mu/main.nf index 5c3492985ef..1da6d7a6576 100644 --- a/target/nextflow/mapping/multi_star_to_h5mu/main.nf +++ b/target/nextflow/mapping/multi_star_to_h5mu/main.nf @@ -258,9 +258,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/multi_star_to_h5mu", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/mapping/samtools_sort/.config.vsh.yaml b/target/nextflow/mapping/samtools_sort/.config.vsh.yaml index 498924d1e72..dedbf23de8e 100644 --- a/target/nextflow/mapping/samtools_sort/.config.vsh.yaml +++ b/target/nextflow/mapping/samtools_sort/.config.vsh.yaml @@ -265,6 +265,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/samtools_sort" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/samtools_sort/samtools_sort" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/mapping/samtools_sort/main.nf b/target/nextflow/mapping/samtools_sort/main.nf index 32a8364364d..4580e8e1798 100644 --- a/target/nextflow/mapping/samtools_sort/main.nf +++ b/target/nextflow/mapping/samtools_sort/main.nf @@ -370,9 +370,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/samtools_sort", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/mapping/star_align/.config.vsh.yaml b/target/nextflow/mapping/star_align/.config.vsh.yaml index 5143629cfe2..5b9a13670cf 100644 --- a/target/nextflow/mapping/star_align/.config.vsh.yaml +++ b/target/nextflow/mapping/star_align/.config.vsh.yaml @@ -2530,6 +2530,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_align" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_align/star_align" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/mapping/star_align/main.nf b/target/nextflow/mapping/star_align/main.nf index 8844450f88f..a01860e8fa0 100644 --- a/target/nextflow/mapping/star_align/main.nf +++ b/target/nextflow/mapping/star_align/main.nf @@ -2644,9 +2644,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_align", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/mapping/star_align_v273a/.config.vsh.yaml b/target/nextflow/mapping/star_align_v273a/.config.vsh.yaml index 99347bf0d98..dcb92f67bbf 100644 --- a/target/nextflow/mapping/star_align_v273a/.config.vsh.yaml +++ b/target/nextflow/mapping/star_align_v273a/.config.vsh.yaml @@ -2530,6 +2530,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_align_v273a" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_align_v273a/star_align_v273a" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/mapping/star_align_v273a/main.nf b/target/nextflow/mapping/star_align_v273a/main.nf index 15f4e2f1d69..03682104bb8 100644 --- a/target/nextflow/mapping/star_align_v273a/main.nf +++ b/target/nextflow/mapping/star_align_v273a/main.nf @@ -2644,9 +2644,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_align_v273a", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/mapping/star_build_reference/.config.vsh.yaml b/target/nextflow/mapping/star_build_reference/.config.vsh.yaml index da86c5a0da4..39f24970175 100644 --- a/target/nextflow/mapping/star_build_reference/.config.vsh.yaml +++ b/target/nextflow/mapping/star_build_reference/.config.vsh.yaml @@ -185,6 +185,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_build_reference" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_build_reference/star_build_reference" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/mapping/star_build_reference/main.nf b/target/nextflow/mapping/star_build_reference/main.nf index 7aa370816b5..9d59580527a 100644 --- a/target/nextflow/mapping/star_build_reference/main.nf +++ b/target/nextflow/mapping/star_build_reference/main.nf @@ -254,9 +254,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_build_reference", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/metadata/add_id/.config.vsh.yaml b/target/nextflow/metadata/add_id/.config.vsh.yaml index 62bb9ff1cab..be9a9a8efa7 100644 --- a/target/nextflow/metadata/add_id/.config.vsh.yaml +++ b/target/nextflow/metadata/add_id/.config.vsh.yaml @@ -192,6 +192,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/add_id" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/add_id/add_id" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/metadata/add_id/main.nf b/target/nextflow/metadata/add_id/main.nf index bfe62162f6e..b298c27a847 100644 --- a/target/nextflow/metadata/add_id/main.nf +++ b/target/nextflow/metadata/add_id/main.nf @@ -276,9 +276,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/add_id", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/metadata/grep_annotation_column/.config.vsh.yaml b/target/nextflow/metadata/grep_annotation_column/.config.vsh.yaml index bbd60ef9603..3a6f571dc37 100644 --- a/target/nextflow/metadata/grep_annotation_column/.config.vsh.yaml +++ b/target/nextflow/metadata/grep_annotation_column/.config.vsh.yaml @@ -239,6 +239,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/grep_annotation_column" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/grep_annotation_column/grep_annotation_column" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/metadata/grep_annotation_column/main.nf b/target/nextflow/metadata/grep_annotation_column/main.nf index 6ee4ec832b6..060de1169c2 100644 --- a/target/nextflow/metadata/grep_annotation_column/main.nf +++ b/target/nextflow/metadata/grep_annotation_column/main.nf @@ -332,9 +332,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/grep_annotation_column", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/metadata/join_csv/.config.vsh.yaml b/target/nextflow/metadata/join_csv/.config.vsh.yaml index debb25b134c..3de4208c579 100644 --- a/target/nextflow/metadata/join_csv/.config.vsh.yaml +++ b/target/nextflow/metadata/join_csv/.config.vsh.yaml @@ -224,6 +224,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/join_csv" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/join_csv/join_csv" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/metadata/join_csv/main.nf b/target/nextflow/metadata/join_csv/main.nf index dd6980bee94..93d41508581 100644 --- a/target/nextflow/metadata/join_csv/main.nf +++ b/target/nextflow/metadata/join_csv/main.nf @@ -313,9 +313,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/join_csv", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/metadata/join_uns_to_obs/.config.vsh.yaml b/target/nextflow/metadata/join_uns_to_obs/.config.vsh.yaml index 684e4a21455..cc71bc00f6f 100644 --- a/target/nextflow/metadata/join_uns_to_obs/.config.vsh.yaml +++ b/target/nextflow/metadata/join_uns_to_obs/.config.vsh.yaml @@ -166,6 +166,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/join_uns_to_obs" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/join_uns_to_obs/join_uns_to_obs" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/metadata/join_uns_to_obs/main.nf b/target/nextflow/metadata/join_uns_to_obs/main.nf index 17f76957ac8..001f201741f 100644 --- a/target/nextflow/metadata/join_uns_to_obs/main.nf +++ b/target/nextflow/metadata/join_uns_to_obs/main.nf @@ -232,9 +232,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/join_uns_to_obs", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml b/target/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml index a8521bf7959..99515d2e742 100644 --- a/target/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml +++ b/target/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml @@ -187,6 +187,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/move_obsm_to_obs" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/move_obsm_to_obs/move_obsm_to_obs" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/metadata/move_obsm_to_obs/main.nf b/target/nextflow/metadata/move_obsm_to_obs/main.nf index 4a7bcc2e348..aebb7c34820 100644 --- a/target/nextflow/metadata/move_obsm_to_obs/main.nf +++ b/target/nextflow/metadata/move_obsm_to_obs/main.nf @@ -270,9 +270,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/move_obsm_to_obs", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/neighbors/bbknn/.config.vsh.yaml b/target/nextflow/neighbors/bbknn/.config.vsh.yaml index 8b7eee4357b..f77d5ae8390 100644 --- a/target/nextflow/neighbors/bbknn/.config.vsh.yaml +++ b/target/nextflow/neighbors/bbknn/.config.vsh.yaml @@ -284,6 +284,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/bbknn" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/bbknn/bbknn" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/neighbors/bbknn/main.nf b/target/nextflow/neighbors/bbknn/main.nf index 35b8f91bc03..b93b848a879 100644 --- a/target/nextflow/neighbors/bbknn/main.nf +++ b/target/nextflow/neighbors/bbknn/main.nf @@ -374,9 +374,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/bbknn", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/neighbors/find_neighbors/.config.vsh.yaml b/target/nextflow/neighbors/find_neighbors/.config.vsh.yaml index 0c77bfa18f6..5a5a678ec3a 100644 --- a/target/nextflow/neighbors/find_neighbors/.config.vsh.yaml +++ b/target/nextflow/neighbors/find_neighbors/.config.vsh.yaml @@ -304,6 +304,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/find_neighbors" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/find_neighbors/find_neighbors" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/neighbors/find_neighbors/main.nf b/target/nextflow/neighbors/find_neighbors/main.nf index e3e2bdc5087..413261c9451 100644 --- a/target/nextflow/neighbors/find_neighbors/main.nf +++ b/target/nextflow/neighbors/find_neighbors/main.nf @@ -399,9 +399,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/find_neighbors", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/process_10xh5/filter_10xh5/.config.vsh.yaml b/target/nextflow/process_10xh5/filter_10xh5/.config.vsh.yaml index a3df1a7d3ff..5a0d1dbef6d 100644 --- a/target/nextflow/process_10xh5/filter_10xh5/.config.vsh.yaml +++ b/target/nextflow/process_10xh5/filter_10xh5/.config.vsh.yaml @@ -190,6 +190,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/process_10xh5/filter_10xh5" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/process_10xh5/filter_10xh5/filter_10xh5" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/process_10xh5/filter_10xh5/main.nf b/target/nextflow/process_10xh5/filter_10xh5/main.nf index 940771bb128..faff379d179 100644 --- a/target/nextflow/process_10xh5/filter_10xh5/main.nf +++ b/target/nextflow/process_10xh5/filter_10xh5/main.nf @@ -267,9 +267,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/process_10xh5/filter_10xh5", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml b/target/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml index 6b8cdea897e..ff0ff847a5a 100644 --- a/target/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml +++ b/target/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml @@ -230,6 +230,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/calculate_qc_metrics" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/calculate_qc_metrics/calculate_qc_metrics" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/qc/calculate_qc_metrics/main.nf b/target/nextflow/qc/calculate_qc_metrics/main.nf index dc474bffdb6..b884cef0609 100644 --- a/target/nextflow/qc/calculate_qc_metrics/main.nf +++ b/target/nextflow/qc/calculate_qc_metrics/main.nf @@ -306,9 +306,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/calculate_qc_metrics", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/qc/fastqc/.config.vsh.yaml b/target/nextflow/qc/fastqc/.config.vsh.yaml index cf030072858..cb068c0f230 100644 --- a/target/nextflow/qc/fastqc/.config.vsh.yaml +++ b/target/nextflow/qc/fastqc/.config.vsh.yaml @@ -151,6 +151,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/fastqc" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/fastqc/fastqc" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/qc/fastqc/main.nf b/target/nextflow/qc/fastqc/main.nf index 415a8b84bb0..0902adc5c64 100644 --- a/target/nextflow/qc/fastqc/main.nf +++ b/target/nextflow/qc/fastqc/main.nf @@ -208,9 +208,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/fastqc", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/qc/multiqc/.config.vsh.yaml b/target/nextflow/qc/multiqc/.config.vsh.yaml index af4d7132d88..99c382ce3a6 100644 --- a/target/nextflow/qc/multiqc/.config.vsh.yaml +++ b/target/nextflow/qc/multiqc/.config.vsh.yaml @@ -135,6 +135,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/multiqc" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/multiqc/multiqc" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/qc/multiqc/main.nf b/target/nextflow/qc/multiqc/main.nf index 17aa3eb9dcf..e4b0858e85f 100644 --- a/target/nextflow/qc/multiqc/main.nf +++ b/target/nextflow/qc/multiqc/main.nf @@ -193,9 +193,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/multiqc", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/query/cellxgene_census/.config.vsh.yaml b/target/nextflow/query/cellxgene_census/.config.vsh.yaml index 988afd74751..7ea63f9e06b 100644 --- a/target/nextflow/query/cellxgene_census/.config.vsh.yaml +++ b/target/nextflow/query/cellxgene_census/.config.vsh.yaml @@ -255,6 +255,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/query/cellxgene_census" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/query/cellxgene_census/cellxgene_census" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/query/cellxgene_census/main.nf b/target/nextflow/query/cellxgene_census/main.nf index 755e2815bf6..0ad390f627a 100644 --- a/target/nextflow/query/cellxgene_census/main.nf +++ b/target/nextflow/query/cellxgene_census/main.nf @@ -353,9 +353,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/query/cellxgene_census", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/reference/build_bdrhap_reference/.config.vsh.yaml b/target/nextflow/reference/build_bdrhap_reference/.config.vsh.yaml index f8178250e2c..7e87683edd5 100644 --- a/target/nextflow/reference/build_bdrhap_reference/.config.vsh.yaml +++ b/target/nextflow/reference/build_bdrhap_reference/.config.vsh.yaml @@ -181,6 +181,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/build_bdrhap_reference" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/build_bdrhap_reference/build_bdrhap_reference" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/reference/build_bdrhap_reference/main.nf b/target/nextflow/reference/build_bdrhap_reference/main.nf index a80c014010a..0135dd2ac1a 100644 --- a/target/nextflow/reference/build_bdrhap_reference/main.nf +++ b/target/nextflow/reference/build_bdrhap_reference/main.nf @@ -267,9 +267,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/build_bdrhap_reference", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/reference/build_cellranger_reference/.config.vsh.yaml b/target/nextflow/reference/build_cellranger_reference/.config.vsh.yaml index 3426303820c..c37de090499 100644 --- a/target/nextflow/reference/build_cellranger_reference/.config.vsh.yaml +++ b/target/nextflow/reference/build_cellranger_reference/.config.vsh.yaml @@ -182,6 +182,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/build_cellranger_reference" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/build_cellranger_reference/build_cellranger_reference" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/reference/build_cellranger_reference/main.nf b/target/nextflow/reference/build_cellranger_reference/main.nf index 3fc04831f36..50b7ce7c806 100644 --- a/target/nextflow/reference/build_cellranger_reference/main.nf +++ b/target/nextflow/reference/build_cellranger_reference/main.nf @@ -268,9 +268,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/build_cellranger_reference", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/reference/make_reference/.config.vsh.yaml b/target/nextflow/reference/make_reference/.config.vsh.yaml index 06c49b364f7..ffa4fde4afc 100644 --- a/target/nextflow/reference/make_reference/.config.vsh.yaml +++ b/target/nextflow/reference/make_reference/.config.vsh.yaml @@ -207,6 +207,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/make_reference" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/make_reference/make_reference" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/reference/make_reference/main.nf b/target/nextflow/reference/make_reference/main.nf index 59111a17a93..d915b934e2c 100644 --- a/target/nextflow/reference/make_reference/main.nf +++ b/target/nextflow/reference/make_reference/main.nf @@ -286,9 +286,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/make_reference", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/report/mermaid/.config.vsh.yaml b/target/nextflow/report/mermaid/.config.vsh.yaml index c0482dafadb..8f07f821e35 100644 --- a/target/nextflow/report/mermaid/.config.vsh.yaml +++ b/target/nextflow/report/mermaid/.config.vsh.yaml @@ -180,6 +180,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/report/mermaid" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/report/mermaid/mermaid" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/report/mermaid/main.nf b/target/nextflow/report/mermaid/main.nf index bba9cfcb288..81597f72fb1 100644 --- a/target/nextflow/report/mermaid/main.nf +++ b/target/nextflow/report/mermaid/main.nf @@ -254,9 +254,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/report/mermaid", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/transfer/publish/.config.vsh.yaml b/target/nextflow/transfer/publish/.config.vsh.yaml index e2b2373f64d..94bb9755a43 100644 --- a/target/nextflow/transfer/publish/.config.vsh.yaml +++ b/target/nextflow/transfer/publish/.config.vsh.yaml @@ -120,6 +120,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transfer/publish" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transfer/publish/publish" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/transfer/publish/main.nf b/target/nextflow/transfer/publish/main.nf index a749b0fcd88..354f635ef87 100644 --- a/target/nextflow/transfer/publish/main.nf +++ b/target/nextflow/transfer/publish/main.nf @@ -176,9 +176,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transfer/publish", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/transform/clr/.config.vsh.yaml b/target/nextflow/transform/clr/.config.vsh.yaml index c0a78e4e408..7d983156f1f 100644 --- a/target/nextflow/transform/clr/.config.vsh.yaml +++ b/target/nextflow/transform/clr/.config.vsh.yaml @@ -183,6 +183,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/clr" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/clr/clr" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/transform/clr/main.nf b/target/nextflow/transform/clr/main.nf index f56529e5886..fbacb5d71a7 100644 --- a/target/nextflow/transform/clr/main.nf +++ b/target/nextflow/transform/clr/main.nf @@ -262,9 +262,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/clr", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/transform/delete_layer/.config.vsh.yaml b/target/nextflow/transform/delete_layer/.config.vsh.yaml index 9015ae1bbb3..c637b0deb48 100644 --- a/target/nextflow/transform/delete_layer/.config.vsh.yaml +++ b/target/nextflow/transform/delete_layer/.config.vsh.yaml @@ -191,6 +191,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/delete_layer" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/delete_layer/delete_layer" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/transform/delete_layer/main.nf b/target/nextflow/transform/delete_layer/main.nf index 7296a6afd5d..bdd4cbb2e5b 100644 --- a/target/nextflow/transform/delete_layer/main.nf +++ b/target/nextflow/transform/delete_layer/main.nf @@ -277,9 +277,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/delete_layer", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/transform/log1p/.config.vsh.yaml b/target/nextflow/transform/log1p/.config.vsh.yaml index 5eb9f701b57..6dfef8173a4 100644 --- a/target/nextflow/transform/log1p/.config.vsh.yaml +++ b/target/nextflow/transform/log1p/.config.vsh.yaml @@ -220,6 +220,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/log1p" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/log1p/log1p" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/transform/log1p/main.nf b/target/nextflow/transform/log1p/main.nf index 84259f19834..018e33275f8 100644 --- a/target/nextflow/transform/log1p/main.nf +++ b/target/nextflow/transform/log1p/main.nf @@ -315,9 +315,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/log1p", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/transform/normalize_total/.config.vsh.yaml b/target/nextflow/transform/normalize_total/.config.vsh.yaml index a37dc877b07..f23f99b8927 100644 --- a/target/nextflow/transform/normalize_total/.config.vsh.yaml +++ b/target/nextflow/transform/normalize_total/.config.vsh.yaml @@ -237,6 +237,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/normalize_total" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/normalize_total/normalize_total" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/transform/normalize_total/main.nf b/target/nextflow/transform/normalize_total/main.nf index c55c9ecc125..3b2ce549a7b 100644 --- a/target/nextflow/transform/normalize_total/main.nf +++ b/target/nextflow/transform/normalize_total/main.nf @@ -324,9 +324,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/normalize_total", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/transform/regress_out/.config.vsh.yaml b/target/nextflow/transform/regress_out/.config.vsh.yaml index 41cdca4fc3f..9bffc20ea66 100644 --- a/target/nextflow/transform/regress_out/.config.vsh.yaml +++ b/target/nextflow/transform/regress_out/.config.vsh.yaml @@ -190,6 +190,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/regress_out" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/regress_out/regress_out" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/transform/regress_out/main.nf b/target/nextflow/transform/regress_out/main.nf index 9e18ca29ea4..53de04a888f 100644 --- a/target/nextflow/transform/regress_out/main.nf +++ b/target/nextflow/transform/regress_out/main.nf @@ -270,9 +270,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/regress_out", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/transform/scale/.config.vsh.yaml b/target/nextflow/transform/scale/.config.vsh.yaml index 205297a5587..5a8ea4ffe27 100644 --- a/target/nextflow/transform/scale/.config.vsh.yaml +++ b/target/nextflow/transform/scale/.config.vsh.yaml @@ -200,6 +200,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/scale" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/scale/scale" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/transform/scale/main.nf b/target/nextflow/transform/scale/main.nf index 583c9a13a98..c731506a950 100644 --- a/target/nextflow/transform/scale/main.nf +++ b/target/nextflow/transform/scale/main.nf @@ -285,9 +285,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/scale", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/velocity/scvelo/.config.vsh.yaml b/target/nextflow/velocity/scvelo/.config.vsh.yaml index 8ed446e7d9b..1032a08d4d1 100644 --- a/target/nextflow/velocity/scvelo/.config.vsh.yaml +++ b/target/nextflow/velocity/scvelo/.config.vsh.yaml @@ -271,6 +271,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/velocity/scvelo" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/velocity/scvelo/scvelo" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/velocity/scvelo/main.nf b/target/nextflow/velocity/scvelo/main.nf index fa04fdbe7de..2f2a020d322 100644 --- a/target/nextflow/velocity/scvelo/main.nf +++ b/target/nextflow/velocity/scvelo/main.nf @@ -365,9 +365,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/velocity/scvelo", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) diff --git a/target/nextflow/velocity/velocyto/.config.vsh.yaml b/target/nextflow/velocity/velocyto/.config.vsh.yaml index 60a7f7b1564..4ebb609e299 100644 --- a/target/nextflow/velocity/velocyto/.config.vsh.yaml +++ b/target/nextflow/velocity/velocyto/.config.vsh.yaml @@ -220,6 +220,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/velocity/velocyto" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/velocity/velocyto/velocyto" viash_version: "0.7.5" - git_commit: "a98b37524a0b7ccc2693db3e2df30d77f7230fd8" + git_commit: "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "0.12.2-2-ga98b37524a" + git_tag: "0.12.2-3-g827d483cf7" diff --git a/target/nextflow/velocity/velocyto/main.nf b/target/nextflow/velocity/velocyto/main.nf index 0d23bd078f9..26248b02f97 100644 --- a/target/nextflow/velocity/velocyto/main.nf +++ b/target/nextflow/velocity/velocyto/main.nf @@ -314,9 +314,9 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/velocity/velocyto", "viash_version" : "0.7.5", - "git_commit" : "a98b37524a0b7ccc2693db3e2df30d77f7230fd8", + "git_commit" : "827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "0.12.2-2-ga98b37524a" + "git_tag" : "0.12.2-3-g827d483cf7" } }''')) From a740017da64075206918cb4d59d9fc315144e86b Mon Sep 17 00:00:00 2001 From: DriesSchaumont <5946712+DriesSchaumont@users.noreply.github.com> Date: Thu, 25 Jan 2024 11:32:39 +0100 Subject: [PATCH 4/4] Revert "Update CI" This reverts commit 827d483cf7d8844f3a3745b724f1d9cdeb3c7a2f. --- .github/workflows/create-documentation-pr.yml | 4 +- .github/workflows/integration-test.yml | 159 +++++++--- .github/workflows/main-build.yml | 280 ++---------------- .github/workflows/release-build-viash-hub.yml | 18 +- .github/workflows/release-build.yml | 17 +- .github/workflows/viash-test.yml | 5 +- 6 files changed, 163 insertions(+), 320 deletions(-) diff --git a/.github/workflows/create-documentation-pr.yml b/.github/workflows/create-documentation-pr.yml index 328cf3a3be6..f3ef7785861 100644 --- a/.github/workflows/create-documentation-pr.yml +++ b/.github/workflows/create-documentation-pr.yml @@ -28,14 +28,14 @@ jobs: uses: viash-io/viash-actions/ns-list@v4 with: platform: docker + src: src format: json - query_namespace: ^(?!workflows) - id: ns_list_workflows uses: viash-io/viash-actions/ns-list@v4 with: + src: workflows format: json - query_namespace: ^workflows - id: set_matrix run: | diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index c2d897c0eed..5258d7a6686 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -1,88 +1,169 @@ name: integration test -concurrency: - group: ${{ github.workflow }} - cancel-in-progress: false on: workflow_dispatch: - inputs: - push_containers: - type: boolean - required: false - default: true - description: Build docker images and push them to the registry schedule: - cron: '33 2 * * *' jobs: - # Build and create containers - build: - uses: ./.github/workflows/main-build.yml - with: - push_containers: ${{ github.event_name == 'schedule' || inputs.push_containers }} - version: 'integration_build' - target_tag: 'integration_build' - deploy_to_viash_hub: false - deploy_branch: 'integration_build' - secrets: inherit - - # Synchronize S3 Bucket and create cache for per-component runs - sync_s3: + # phase 1 + list: env: s3_bucket: s3://openpipelines-data/ runs-on: ubuntu-latest outputs: + component_matrix: ${{ steps.set_matrix.outputs.components }} + workflow_matrix: ${{ steps.set_matrix.outputs.workflows }} cache_key: ${{ steps.cache.outputs.cache_key }} steps: + - uses: actions/checkout@v4 + + - uses: viash-io/viash-actions/setup@v4 + - uses: viash-io/viash-actions/project/sync-and-cache-s3@v4 - id: cache + id: cache with: s3_bucket: $s3_bucket dest_path: resources_test cache_key_prefix: resources_test__ - # phase 3 - integration_test: + - name: Remove target folder from .gitignore + run: | + # allow publishing the target folder + sed -i '/^\/target\/$/d' .gitignore + + - uses: viash-io/viash-actions/ns-build@v4 + with: + config_mod: .functionality.version := 'integration_build' + parallel: true + + - name: Deploy to target branch + uses: peaceiris/actions-gh-pages@v3 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: . + publish_branch: integration_build + exclude_assets: '' + + - id: ns_list_components + uses: viash-io/viash-actions/ns-list@v4 + with: + platform: docker + src: src + format: json + + - id: ns_list_workflows + uses: viash-io/viash-actions/ns-list@v4 + with: + src: workflows + format: json + + - id: set_matrix + run: | + echo "components=$(jq -c '[ .[] | + { + "name": (.functionality.namespace + (.platforms | map(select(.type == "docker"))[0].namespace_separator) + .functionality.name), + "config": .info.config, + "dir": .info.config | capture("^(?.*\/)").dir + } + ]' ${{ steps.ns_list_components.outputs.output_file }} )" >> $GITHUB_OUTPUT + + echo "workflows=$(jq -c '[ .[] | . as $config | (.functionality.test_resources // [])[] | select(.type == "nextflow_script", .entrypoint) | + { + "name": ($config.functionality.namespace + "/" + $config.functionality.name), + "main_script": (($config.info.config | capture("^(?.*\/)").dir) + "/" + .path), + "entry": .entrypoint, + "config": $config.info.config + } + ] | unique' ${{ steps.ns_list_workflows.outputs.output_file }} )" >> $GITHUB_OUTPUT + + # phase 2 + build: + needs: list + runs-on: ubuntu-latest - needs: [ build, sync_s3 ] - if: "${{ needs.build.outputs.workflow_matrix != '[]' }}" strategy: fail-fast: false matrix: - component: ${{ fromJson(needs.build.outputs.workflow_matrix) }} + component: ${{ fromJson(needs.list.outputs.component_matrix) }} steps: # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' - uses: data-intuitive/reclaim-the-bytes@v2 - - name: Keep symlinks as-is - run: | - git config --global core.symlinks true - - uses: actions/checkout@v4 + + - uses: viash-io/viash-actions/setup@v4 + + - name: Build container + uses: viash-io/viash-actions/ns-build@v4 + with: + config_mod: .functionality.version := 'integration_build' + setup: build + src: ${{ matrix.component.dir }} + + - name: Login to container registry + uses: docker/login-action@v3 + with: + registry: ghcr.io + username: ${{ secrets.GTHB_USER }} + password: ${{ secrets.GTHB_PAT }} + + - name: Push container + uses: viash-io/viash-actions/ns-build@v4 with: - ref: 'integration_build' + config_mod: .functionality.version := 'integration_build' + platform: docker + src: ${{ matrix.component.dir }} + setup: push + + ################################### + # phase 3 + integration_test: + needs: [ build, list ] + if: "${{ needs.list.outputs.workflow_matrix != '[]' }}" + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + component: ${{ fromJson(needs.list.outputs.workflow_matrix) }} + + steps: + # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' + - uses: data-intuitive/reclaim-the-bytes@v2 + + - uses: actions/checkout@v4 - uses: viash-io/viash-actions/setup@v4 - - uses: nf-core/setup-nextflow@v1.5.0 + - uses: nf-core/setup-nextflow@v1.3.0 + + # build target dir + # use containers from integration_build branch, hopefully these are available + - name: Build target dir + uses: viash-io/viash-actions/ns-build@v4 + with: + config_mod: ".functionality.version := 'integration_build'" + parallel: true # use cache - name: Cache resources data - uses: actions/cache@v4 + uses: actions/cache@v3 timeout-minutes: 5 with: path: resources_test - key: ${{ needs.sync_s3.outputs.cache_key }} + key: ${{ needs.list.outputs.cache_key }} fail-on-cache-miss: true - name: Remove unused test resources to save space shell: bash run: | - readarray -t resources < <(viash config view --format json "${{ matrix.component.config }}" -c 'del(.functionality.dependencies)' | jq -r -c '(.info.config | capture("^(?.*\/)").dir) as $dir | .functionality.test_resources | map(select(.type == "file")) | map($dir + .path) | unique | .[]') + readarray -t resources < <(viash config view --format json "${{ matrix.component.config }}" | jq -r -c '(.info.config | capture("^(?.*\/)").dir) as $dir | .functionality.test_resources | map(select(.type == "file")) | map($dir + .path) | unique | .[]') to_not_remove=() for resource in "${resources[@]}"; do if [[ $resource == *"resources_test"* ]]; then @@ -97,9 +178,7 @@ jobs: unset 'to_not_remove[${#to_not_remove[@]}-1]' to_not_remove+=( "(" "${to_not_remove[@]}" ")" "-prune" "-o") fi - echo "Not removing ${to_not_remove[@]}" find ./resources_test/ "${to_not_remove[@]}" -type f -exec rm {} + - tree ./resources_test/ - name: Run integration test timeout-minutes: 60 @@ -110,4 +189,4 @@ jobs: -main-script "${{ matrix.component.main_script }}" \ -entry "${{ matrix.component.entry }}" \ -profile docker,mount_temp,no_publish \ - -c src/workflows/utils/labels_ci.config + -c workflows/utils/labels_ci.config diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 758a4d1127e..536e8743ed6 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -1,136 +1,24 @@ -name: Build +name: main build concurrency: - group: ${{ github.workflow }}-${{ github.event.inputs.deploy_branch && format('{0}_build', github.ref_name) || github.event.inputs.deploy_branch }} + group: main_build cancel-in-progress: true on: - workflow_dispatch: - inputs: - push_containers: - type: boolean - required: false - default: false - description: Build docker images and push them to the registry - version: - type: string - required: false - description: | - Version to tag the build components with (e.i functionality.version). - Defaults to name of the branch that triggered the workflow, suffixed by "_build". - target_tag: - type: string - required: false - default: main_build - description: | - Version tag of containers to use. Is `main_build` by default. - Can be used in combination with 'push_containers' to re-use existing docker images - or set the tag for new builds. - deploy_to_viash_hub: - type: boolean - required: false - default: false - description: Also build packages and docker images for viash-hub.com and push them. - - # when used as a subworkflow - workflow_call: - inputs: - push_containers: - type: boolean - required: false - default: false - description: push the containers to the registry - version: - type: string - required: false - description: | - Version to tag the build components with (e.i functionality.version). - Defaults to name of the branch that triggered the workflow, suffixed by "_build". - target_tag: - type: string - required: false - default: main_build - description: Version tag of existing containers to use. Is `main_build` by default. - deploy_branch: - type: string - required: false - description: | - Branch to deploy the build to. Defaults to name of the branch - that triggered the workflow, suffixed by "_build". - deploy_to_viash_hub: - type: boolean - required: false - default: false - description: Also build packages and docker images for viash-hub.com and push them. - outputs: - component_matrix: - description: "A JSON object that can be used to populate a github actions matrix for component jobs." - value: ${{ jobs.build_and_deploy_target_folder.outputs.component_matrix }} - workflow_matrix: - description: "A JSON object that can be used to populate a github actions matrix for workflow jobs." - value: ${{ jobs.build_and_deploy_target_folder.outputs.workflow_matrix}} - secrets: - VIASHHUB_USER: - required: true - VIASHHUB_PAT: - required: true - GTHB_USER: - required: true - GTHB_PAT: - required: true push: branches: [ 'main' ] - jobs: # phase 1 - build_and_deploy_target_folder: - name: "Build and push target folder" + list: runs-on: ubuntu-latest outputs: - component_matrix: ${{ steps.set_matrix.outputs.components }} - workflow_matrix: ${{ steps.set_matrix.outputs.workflows }} - - env: - DEPLOY_BRANCH: ${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }} + component_matrix: ${{ steps.set_matrix.outputs.matrix }} + cache_key: ${{ steps.cache.outputs.cache_key }} steps: - - name: Keep symlinks as-is - run: | - git config --global core.symlinks true - - - uses: actions/checkout@v4 - if: ${{ inputs.deploy_to_viash_hub == 'true' }} - with: - fetch-depth: 0 - - - name: Push ref to Viash-hub - if: ${{ inputs.deploy_to_viash_hub == 'true' }} - run: | - git remote add viash-hub https://x-access-token:${{ secrets.VIASHHUB_PAT }}@viash-hub.com/openpipelines-bio/openpipeline.git - git push -f -u viash-hub ${{ github.ref_name }} - - - name: Branch to checkout (use existing target branch if it exists) - id: get_checkout_branch - run: | - if ! git ls-remote --heads --exit-code https://github.com/openpipelines-bio/openpipeline.git "$DEPLOY_BRANCH" > /dev/null; then - echo "Remote branch does not exist, fetching current branch and building on top of it" - echo "checkout_branch=${{ github.ref_name }}" >> "$GITHUB_OUTPUT" - else - echo "Remote branch exists, checking out existing branch" - echo "checkout_branch=$DEPLOY_BRANCH" >> "$GITHUB_OUTPUT" - fi - - uses: actions/checkout@v4 - with: - ref: ${{ steps.get_checkout_branch.outputs.checkout_branch }} - fetch-depth: 0 - - name: Fetch changes from ${{github.ref_name}} - run: | - git fetch origin ${{github.ref_name}} - git checkout -f --no-overlay origin/${{github.ref_name}} -- '.' - - uses: viash-io/viash-actions/setup@v4 - name: Remove target folder from .gitignore @@ -140,62 +28,43 @@ jobs: - uses: viash-io/viash-actions/ns-build@v4 with: - config_mod: | - .functionality.version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" - .platforms[.type == 'docker'].target_tag := '${{ github.event_name == 'push' && 'main_build' || inputs.target_tag }}' + config_mod: .functionality.version := 'main_build' parallel: true - query: ^(?!workflows) - - - uses: viash-io/viash-actions/ns-build@v4 - with: - config_mod: .functionality.version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" - parallel: true - query: ^workflows - + - name: Build nextflow schemas uses: viash-io/viash-actions/pro/build-nextflow-schemas@v4 with: + workflows: workflows components: src - workflows: src viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' - name: Build parameter files uses: viash-io/viash-actions/pro/build-nextflow-params@v4 with: - workflows: src + workflows: workflows components: src viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' - name: Deploy to target branch - uses: stefanzweifel/git-auto-commit-action@v5 - with: - create_branch: true - commit_message: "deploy: ${{github.sha}}" - skip_dirty_check: true - branch: ${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }} - - name: "List components" - id: ns_list - uses: viash-io/viash-actions/ns-list@v4 + uses: peaceiris/actions-gh-pages@v3 with: - platform: docker - src: src - format: json - query_namespace: ^(?!workflows) + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: . + publish_branch: main_build + exclude_assets: '' - - name: "List workflows" - id: ns_list_workflows + - id: ns_list uses: viash-io/viash-actions/ns-list@v4 with: + platform: docker src: src format: json - query_namespace: ^workflows - - name: "Parse JSON output from 'viash ns list' as input for matrix." - id: set_matrix + - id: set_matrix run: | - echo "components=$(jq -c '[ .[] | + echo "matrix=$(jq -c '[ .[] | { "name": (.functionality.namespace + "/" + .functionality.name), "config": .info.config, @@ -203,82 +72,16 @@ jobs: } ]' ${{ steps.ns_list.outputs.output_file }} )" >> $GITHUB_OUTPUT - echo "workflows=$(jq -c '[ .[] | . as $config | (.functionality.test_resources // [])[] | select(.type == "nextflow_script", .entrypoint) | - { - "name": ($config.functionality.namespace + "/" + $config.functionality.name), - "main_script": (($config.info.config | capture("^(?.*\/)").dir) + "/" + .path), - "entry": .entrypoint, - "config": $config.info.config - } - ] | unique' ${{ steps.ns_list_workflows.outputs.output_file }} )" >> $GITHUB_OUTPUT - - - uses: actions/checkout@v4 - if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} - with: - ref: ${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }} - fetch-depth: 0 - clean: true - - - name: Set origin to viash-hub and commit on top of it. - if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} - # This is needed because git-auto-commit-action uses origin by default - run: | - git remote add viash-hub https://x-access-token:${{ secrets.VIASHHUB_PAT }}@viash-hub.com/openpipelines-bio/openpipeline.git - if git ls-remote --heads --exit-code https://viash-hub.com/openpipelines-bio/openpipeline.git ${{ github.ref_name }}_build > /dev/null; then - git fetch viash-hub ${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }} - git reset --hard viash-hub/${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }} - fi - git checkout -f --no-overlay origin/${{github.ref_name}} -- '.' - git remote set-url origin https://x-access-token:${{ secrets.VIASHHUB_PAT }}@viash-hub.com/openpipelines-bio/openpipeline.git - git remote rm viash-hub - - - name: Remove target folder from .gitignore - run: | - # allow publishing the target folder - sed -i '/^\/target\/$/d' .gitignore - - - uses: viash-io/viash-actions/ns-build@v4 - if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} - with: - config_mod: | - .functionality.version := " ${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }}" - .platforms[.type == 'docker'].target_tag := '${{ github.event_name == 'push' && 'main_build' || inputs.target_tag }}' - .platforms[.type == 'docker'].target_organization := 'openpipelines-bio/openpipeline' - .platforms[.type == 'docker'].target_registry := 'viash-hub.com:5050' - .platforms[.type == 'docker'].target_image_source := 'https://viash-hub.com/openpipelines-bio/openpipeline' - parallel: true - query: ^(?!workflows) - - - uses: viash-io/viash-actions/ns-build@v4 - if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} - with: - config_mod: | - .functionality.version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" - parallel: true - query: ^workflows - - - name: Deploy to target branch - if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} - uses: stefanzweifel/git-auto-commit-action@v5 - with: - create_branch: true - commit_message: "deploy: ${{github.sha}}" - skip_dirty_check: true - branch: ${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }} - skip_checkout: true - # phase 2 - build_and_deploy_docker_containers: - name: "Build and Deploy Docker Images" - needs: build_and_deploy_target_folder - if: ${{github.event_name == 'push' || inputs.push_containers }} + build: + needs: list runs-on: ubuntu-latest strategy: fail-fast: false matrix: - component: ${{ fromJson(needs.build_and_deploy_target_folder.outputs.component_matrix) }} + component: ${{ fromJson(needs.list.outputs.component_matrix) }} steps: # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' @@ -291,9 +94,7 @@ jobs: - name: Build container uses: viash-io/viash-actions/ns-build@v4 with: - config_mod: | - .functionality.version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" - .platforms[.type == 'docker'].target_tag := '${{ github.event_name == 'push' && 'main_build' || inputs.target_tag }}' + config_mod: .functionality.version := 'main_build' platform: docker src: ${{ matrix.component.dir }} setup: build @@ -308,40 +109,7 @@ jobs: - name: Push container uses: viash-io/viash-actions/ns-build@v4 with: - config_mod: .functionality.version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" - platform: docker - src: ${{ matrix.component.dir }} - setup: push - - - name: Login to Viash-Hub container registry - if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} - uses: docker/login-action@v3 - with: - registry: viash-hub.com:5050 - username: ${{ secrets.VIASHHUB_USER }} - password: ${{ secrets.VIASHHUB_PAT }} - - - name: Update Docker settings - if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} - run: | - sudo sed -i 's/ }/, \"max-concurrent-uploads\": 2 }/' /etc/docker/daemon.json - sudo systemctl restart docker - - - name: "Re-tag containers for viash-hub" - if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} - run: | - viash ns exec -s ${{ matrix.component.dir }} --apply_platform -p docker \ - 'docker tag ghcr.io/openpipelines-bio/{namespace}_{functionality-name}:${{ github.event_name == 'push' && 'main_build' || inputs.target_tag }} viash-hub.com:5050/openpipelines-bio/openpipeline/{namespace}_{functionality-name}:${{ github.ref_name }}_build' - - - name: Push container to Viash-Hub - if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} - uses: viash-io/viash-actions/ns-build@v4 - with: - config_mod: | - .functionality.version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" - .platforms[.type == 'docker'].target_registry := 'viash-hub.com:5050' - .platforms[.type == 'docker'].target_organization := 'openpipelines-bio/openpipeline' - .platforms[.type == 'docker'].target_image_source := 'https://viash-hub.com/openpipelines-bio/openpipeline' + config_mod: .functionality.version := 'main_build' platform: docker src: ${{ matrix.component.dir }} - setup: push + setup: push \ No newline at end of file diff --git a/.github/workflows/release-build-viash-hub.yml b/.github/workflows/release-build-viash-hub.yml index 2c44040d73b..382909746c9 100644 --- a/.github/workflows/release-build-viash-hub.yml +++ b/.github/workflows/release-build-viash-hub.yml @@ -49,13 +49,11 @@ jobs: .platforms[.type == 'docker'].target_organization := 'openpipelines-bio/openpipeline' .platforms[.type == 'docker'].target_image_source := 'https://viash-hub.com/openpipelines-bio/openpipeline' parallel: true - query_namespace: ^(?!workflows) - - name: Build nextflow schemas uses: viash-io/viash-actions/pro/build-nextflow-schemas@v4 with: - workflows: src + workflows: workflows components: src viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' @@ -63,7 +61,7 @@ jobs: - name: Build parameter files uses: viash-io/viash-actions/pro/build-nextflow-params@v4 with: - workflows: src + workflows: workflows components: src viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' @@ -83,14 +81,14 @@ jobs: uses: viash-io/viash-actions/ns-list@v4 with: platform: docker + src: src format: json - query_namespace: ^(?!workflows) - id: ns_list_workflows uses: viash-io/viash-actions/ns-list@v4 with: + src: workflows format: json - query_namespace: ^workflows - id: set_matrix run: | @@ -183,7 +181,7 @@ jobs: - uses: viash-io/viash-actions/setup@v4 - - uses: nf-core/setup-nextflow@v1.5.0 + - uses: nf-core/setup-nextflow@v1.3.0 # build target dir # use containers from release branch, hopefully these are available @@ -200,7 +198,7 @@ jobs: # use cache - name: Cache resources data - uses: actions/cache@v4 + uses: actions/cache@v3 timeout-minutes: 5 with: path: resources_test @@ -236,7 +234,7 @@ jobs: -main-script "${{ matrix.component.main_script }}" \ -entry ${{ matrix.component.entry }} \ -profile docker,mount_temp,no_publish \ - -c src/workflows/utils/labels_ci.config + -c workflows/utils/labels_ci.config ###################################3 # phase 4 @@ -261,7 +259,7 @@ jobs: # use cache - name: Cache resources data id: restore_cache - uses: actions/cache/restore@v4 + uses: actions/cache/restore@v3 env: SEGMENT_DOWNLOAD_TIMEOUT_MINS: 5 with: diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index 3fbf7f1c1b4..a92d51c990f 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -40,12 +40,11 @@ jobs: with: config_mod: ".functionality.version := '${{ github.event.inputs.version_tag }}'" parallel: true - query_namespace: ^(?!workflows) - name: Build nextflow schemas uses: viash-io/viash-actions/pro/build-nextflow-schemas@v4 with: - workflows: src + workflows: workflows components: src viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' @@ -53,7 +52,7 @@ jobs: - name: Build parameter files uses: viash-io/viash-actions/pro/build-nextflow-params@v4 with: - workflows: src + workflows: workflows components: src viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' @@ -72,14 +71,14 @@ jobs: uses: viash-io/viash-actions/ns-list@v4 with: platform: docker + src: src format: json - query_namespace: ^(?!workflows) - id: ns_list_workflows uses: viash-io/viash-actions/ns-list@v4 with: + src: workflows format: json - query_namespace: ^workflows - id: set_matrix run: | @@ -164,7 +163,7 @@ jobs: - uses: viash-io/viash-actions/setup@v4 - - uses: nf-core/setup-nextflow@v1.5.0 + - uses: nf-core/setup-nextflow@v1.3.0 # build target dir # use containers from release branch, hopefully these are available @@ -177,7 +176,7 @@ jobs: # use cache - name: Cache resources data - uses: actions/cache@v4 + uses: actions/cache@v3 timeout-minutes: 5 with: path: resources_test @@ -213,7 +212,7 @@ jobs: -main-script "${{ matrix.component.main_script }}" \ -entry ${{ matrix.component.entry }} \ -profile docker,mount_temp,no_publish \ - -c src/workflows/utils/labels_ci.config + -c workflows/utils/labels_ci.config ###################################3 # phase 4 @@ -238,7 +237,7 @@ jobs: # use cache - name: Cache resources data id: restore_cache - uses: actions/cache/restore@v4 + uses: actions/cache/restore@v3 env: SEGMENT_DOWNLOAD_TIMEOUT_MINS: 5 with: diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 05033a85072..369a51db013 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -56,7 +56,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v42 + uses: tj-actions/changed-files@v39 with: separator: ";" diff_relative: true @@ -66,7 +66,6 @@ jobs: with: platform: docker format: json - query_namespace: ^(?!workflows) - id: ns_list_filtered uses: viash-io/viash-actions/project/detect-changed-components@v4 @@ -105,7 +104,7 @@ jobs: # use cache - name: Cache resources data id: restore_cache - uses: actions/cache/restore@v4 + uses: actions/cache/restore@v3 env: SEGMENT_DOWNLOAD_TIMEOUT_MINS: 5 with: