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..7b746fb3075 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -38,6 +38,7 @@ jobs: with: config_mod: .functionality.version := 'integration_build' parallel: true + query_namespace: '^(?!workflows)' - name: Deploy to target branch uses: peaceiris/actions-gh-pages@v3 @@ -51,14 +52,14 @@ 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: | @@ -189,4 +190,4 @@ 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-viash-hub.yml b/.github/workflows/main-build-viash-hub.yml index 9a16834a79d..903a6621cda 100644 --- a/.github/workflows/main-build-viash-hub.yml +++ b/.github/workflows/main-build-viash-hub.yml @@ -39,11 +39,12 @@ 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' @@ -51,7 +52,7 @@ 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' @@ -72,6 +73,7 @@ jobs: platform: docker src: src format: json + query_namespace: ^(?!workflows) - id: set_matrix run: | diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 536e8743ed6..deb6fc7c490 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -30,19 +30,20 @@ jobs: with: config_mod: .functionality.version := 'main_build' 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' @@ -61,6 +62,7 @@ jobs: platform: docker src: src format: json + query_namespace: ^(?!workflows) - id: set_matrix run: | diff --git a/.github/workflows/release-build-viash-hub.yml b/.github/workflows/release-build-viash-hub.yml index 382909746c9..2c736115dee 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: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' @@ -81,14 +83,14 @@ jobs: uses: viash-io/viash-actions/ns-list@v4 with: platform: docker - src: src format: json + query_namespace: ^(?!workflows) - id: ns_list_workflows uses: viash-io/viash-actions/ns-list@v4 with: - src: workflows format: json + query_namespace: ^workflows - id: set_matrix run: | @@ -234,7 +236,7 @@ jobs: -main-script "${{ matrix.component.main_script }}" \ -entry ${{ matrix.component.entry }} \ -profile docker,mount_temp,no_publish \ - -c workflows/utils/labels_ci.config + -c src/workflows/utils/labels_ci.config ###################################3 # phase 4 diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index a92d51c990f..2b0a1a456fd 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -40,11 +40,12 @@ jobs: with: config_mod: ".functionality.version := '${{ 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: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' @@ -71,14 +72,14 @@ jobs: uses: viash-io/viash-actions/ns-list@v4 with: platform: docker - src: src format: json + query_namespace: ^(?!workflows) - id: ns_list_workflows uses: viash-io/viash-actions/ns-list@v4 with: - src: workflows format: json + query_namespace: ^workflows - id: set_matrix run: | @@ -212,7 +213,7 @@ jobs: -main-script "${{ 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 diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 369a51db013..08bad42d972 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -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 diff --git a/CHANGELOG.md b/CHANGELOG.md index 7275134f8b7..355521d3760 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,11 @@ This project now uses viash version 0.8.0 to build components and workflows. Mov * All pipelines no longer use the anonymous workflow. Instead, these workflows were given a name which was added to the viash config as the entrypoint to the pipeline (PR #598). +* Removed the `workflows` folder and moved its contents to new locations (PR #605): + 1. The `resources_test_scripts` folder now resides in the root of the project. + 2. All workflows have been moved to the `src/workflows` folder. + 3. Adjust GitHub Actions to account for new workflow paths. + # openpipelines 0.12.0 ## BREAKING CHANGES diff --git a/workflows/resources_test_scripts/10x_5k_anticmv.sh b/resources_test_scripts/10x_5k_anticmv.sh similarity index 95% rename from workflows/resources_test_scripts/10x_5k_anticmv.sh rename to resources_test_scripts/10x_5k_anticmv.sh index d33d96db132..be66c85ce43 100755 --- a/workflows/resources_test_scripts/10x_5k_anticmv.sh +++ b/resources_test_scripts/10x_5k_anticmv.sh @@ -104,8 +104,8 @@ nextflow \ -resume \ -profile docker,mount_temp \ -params-file /tmp/params.yaml \ - -c workflows/utils/labels.config \ - -c workflows/utils/errorstrat_ignore.config + -c src/workflows/utils/labels.config \ + -c src/workflows/utils/errorstrat_ignore.config # Create h5mu cat > /tmp/params.yaml << HERE @@ -121,7 +121,7 @@ nextflow \ -resume \ -profile docker,mount_temp \ -params-file /tmp/params.yaml \ - -c workflows/utils/labels.config + -c src/workflows/utils/labels.config cat > /tmp/params.yaml << HERE id: "$ID" @@ -133,11 +133,11 @@ HERE # Run full pipeline nextflow \ run . \ - -main-script workflows/multiomics/full_pipeline/main.nf \ + -main-script src/workflows/multiomics/full_pipeline/main.nf \ -resume \ -profile docker,mount_temp \ -params-file /tmp/params.yaml \ - -c workflows/utils/labels.config + -c src/workflows/utils/labels.config # create fastqc directory fastqc_dir="$OUT/fastqc" diff --git a/workflows/resources_test_scripts/10x_5k_lung_crispr.sh b/resources_test_scripts/10x_5k_lung_crispr.sh similarity index 99% rename from workflows/resources_test_scripts/10x_5k_lung_crispr.sh rename to resources_test_scripts/10x_5k_lung_crispr.sh index d7f6b499812..9115deb0e2b 100755 --- a/workflows/resources_test_scripts/10x_5k_lung_crispr.sh +++ b/resources_test_scripts/10x_5k_lung_crispr.sh @@ -115,4 +115,4 @@ nextflow \ -resume \ -profile docker,mount_temp \ -params-file /tmp/params.yaml \ - -c workflows/utils/labels.config \ No newline at end of file + -c src/workflows/utils/labels.config \ No newline at end of file diff --git a/workflows/resources_test_scripts/annotation_test_data.sh b/resources_test_scripts/annotation_test_data.sh similarity index 100% rename from workflows/resources_test_scripts/annotation_test_data.sh rename to resources_test_scripts/annotation_test_data.sh diff --git a/workflows/resources_test_scripts/aws_sync.sh b/resources_test_scripts/aws_sync.sh similarity index 100% rename from workflows/resources_test_scripts/aws_sync.sh rename to resources_test_scripts/aws_sync.sh diff --git a/workflows/resources_test_scripts/bdrhap_5kjrt.sh b/resources_test_scripts/bdrhap_5kjrt.sh similarity index 97% rename from workflows/resources_test_scripts/bdrhap_5kjrt.sh rename to resources_test_scripts/bdrhap_5kjrt.sh index 2462ee987e1..46f789ef820 100755 --- a/workflows/resources_test_scripts/bdrhap_5kjrt.sh +++ b/resources_test_scripts/bdrhap_5kjrt.sh @@ -146,10 +146,10 @@ HERE nextflow \ run . \ - -main-script workflows/ingestion/bd_rhapsody/main.nf \ + -main-script src/workflows/ingestion/bd_rhapsody/main.nf \ -resume \ -profile docker,mount_temp \ -with-trace work/trace.txt \ -params-file /tmp/params.yaml \ - -c workflows/utils/labels.config \ - -c workflows/utils/errorstrat_ignore.config + -c src/orkflows/utils/labels.config \ + -c src/workflows/utils/errorstrat_ignore.config diff --git a/workflows/resources_test_scripts/bdrhap_vdj.sh b/resources_test_scripts/bdrhap_vdj.sh similarity index 92% rename from workflows/resources_test_scripts/bdrhap_vdj.sh rename to resources_test_scripts/bdrhap_vdj.sh index 0967478b3d6..bdefde5e871 100755 --- a/workflows/resources_test_scripts/bdrhap_vdj.sh +++ b/resources_test_scripts/bdrhap_vdj.sh @@ -63,10 +63,10 @@ HERE # run bd rhapsody pipeline nextflow \ run . \ - -main-script workflows/ingestion/bd_rhapsody/main.nf \ + -main-script src/workflows/ingestion/bd_rhapsody/main.nf \ -resume \ -profile docker,mount_temp \ -with-trace work/trace.txt \ -params-file /tmp/params.yaml \ - -c workflows/utils/labels.config \ - -c workflows/utils/errorstrat_ignore.config \ No newline at end of file + -c src/workflows/utils/labels.config \ + -c src/workflows/utils/errorstrat_ignore.config \ No newline at end of file diff --git a/workflows/resources_test_scripts/cellranger_tiny_bcl.sh b/resources_test_scripts/cellranger_tiny_bcl.sh similarity index 100% rename from workflows/resources_test_scripts/cellranger_tiny_bcl.sh rename to resources_test_scripts/cellranger_tiny_bcl.sh diff --git a/workflows/resources_test_scripts/cellranger_tiny_fastq.sh b/resources_test_scripts/cellranger_tiny_fastq.sh similarity index 100% rename from workflows/resources_test_scripts/cellranger_tiny_fastq.sh rename to resources_test_scripts/cellranger_tiny_fastq.sh diff --git a/workflows/resources_test_scripts/concat_test_data.sh b/resources_test_scripts/concat_test_data.sh similarity index 100% rename from workflows/resources_test_scripts/concat_test_data.sh rename to resources_test_scripts/concat_test_data.sh diff --git a/workflows/resources_test_scripts/hlca_reference_model.sh b/resources_test_scripts/hlca_reference_model.sh similarity index 100% rename from workflows/resources_test_scripts/hlca_reference_model.sh rename to resources_test_scripts/hlca_reference_model.sh diff --git a/workflows/resources_test_scripts/merge_test_data.sh b/resources_test_scripts/merge_test_data.sh similarity index 100% rename from workflows/resources_test_scripts/merge_test_data.sh rename to resources_test_scripts/merge_test_data.sh diff --git a/workflows/resources_test_scripts/pbmc_1k_protein_v3.sh b/resources_test_scripts/pbmc_1k_protein_v3.sh similarity index 93% rename from workflows/resources_test_scripts/pbmc_1k_protein_v3.sh rename to resources_test_scripts/pbmc_1k_protein_v3.sh index 5b813ba9427..26ca38c8557 100755 --- a/workflows/resources_test_scripts/pbmc_1k_protein_v3.sh +++ b/resources_test_scripts/pbmc_1k_protein_v3.sh @@ -54,7 +54,7 @@ target/docker/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu \ # run single sample NXF_VER=21.10.6 nextflow \ run . \ - -main-script workflows/multiomics/rna_singlesample/main.nf \ + -main-script src/workflows/multiomics/rna_singlesample/main.nf \ -profile docker \ --id pbmc_1k_protein_v3_uss \ --input "${OUT}_filtered_feature_bc_matrix.h5mu" \ @@ -65,7 +65,7 @@ NXF_VER=21.10.6 nextflow \ # run multisample NXF_VER=21.10.6 nextflow \ run . \ - -main-script workflows/multiomics/rna_multisample/main.nf \ + -main-script src/workflows/multiomics/rna_multisample/main.nf \ -profile docker \ --id pbmc_1k_protein_v3_ums \ --input "${OUT}_uss.h5mu" \ @@ -76,7 +76,7 @@ NXF_VER=21.10.6 nextflow \ # run integration NXF_VER=21.10.6 nextflow \ run . \ - -main-script workflows/multiomics/integration/main.nf \ + -main-script src/workflows/multiomics/integration/main.nf \ -profile docker \ --id pbmc_1k_protein_v3_mms \ --input "${OUT}_ums.h5mu" \ diff --git a/workflows/resources_test_scripts/ref_gencodev41_chr1.sh b/resources_test_scripts/ref_gencodev41_chr1.sh similarity index 93% rename from workflows/resources_test_scripts/ref_gencodev41_chr1.sh rename to resources_test_scripts/ref_gencodev41_chr1.sh index 9111949f711..a56f34b9ef9 100755 --- a/workflows/resources_test_scripts/ref_gencodev41_chr1.sh +++ b/resources_test_scripts/ref_gencodev41_chr1.sh @@ -15,7 +15,7 @@ wget "https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip" -O "$OU NXF_VER=21.10.6 nextflow \ run . \ - -main-script workflows/ingestion/make_reference/main.nf \ + -main-script src/workflows/ingestion/make_reference/main.nf \ -profile docker \ --id "$ID" \ --genome_fasta "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/GRCh38.primary_assembly.genome.fa.gz" \ diff --git a/workflows/resources_test_scripts/remote_param_list.sh b/resources_test_scripts/remote_param_list.sh similarity index 100% rename from workflows/resources_test_scripts/remote_param_list.sh rename to resources_test_scripts/remote_param_list.sh diff --git a/workflows/resources_test_scripts/rna_velocity.sh b/resources_test_scripts/rna_velocity.sh similarity index 100% rename from workflows/resources_test_scripts/rna_velocity.sh rename to resources_test_scripts/rna_velocity.sh diff --git a/workflows/.gitignore b/src/workflows/.gitignore similarity index 100% rename from workflows/.gitignore rename to src/workflows/.gitignore diff --git a/workflows/ingestion/bd_rhapsody/config.vsh.yaml b/src/workflows/ingestion/bd_rhapsody/config.vsh.yaml similarity index 98% rename from workflows/ingestion/bd_rhapsody/config.vsh.yaml rename to src/workflows/ingestion/bd_rhapsody/config.vsh.yaml index b465b784fe0..71fd0f2477d 100644 --- a/workflows/ingestion/bd_rhapsody/config.vsh.yaml +++ b/src/workflows/ingestion/bd_rhapsody/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "bd_rhapsody" - namespace: "ingestion" + namespace: "workflows/ingestion" description: | A wrapper for the BD Rhapsody Analysis CWL v1.10.1 pipeline. @@ -153,4 +153,6 @@ functionality: path: main.nf entrypoint: test_wf - path: /resources_test/bdrhap_5kjrt - - path: /resources_test/reference_gencodev41_chr1/ \ No newline at end of file + - path: /resources_test/reference_gencodev41_chr1/ +platforms: + - type: nextflow \ No newline at end of file diff --git a/workflows/ingestion/bd_rhapsody/integration_test.sh b/src/workflows/ingestion/bd_rhapsody/integration_test.sh similarity index 100% rename from workflows/ingestion/bd_rhapsody/integration_test.sh rename to src/workflows/ingestion/bd_rhapsody/integration_test.sh diff --git a/workflows/ingestion/bd_rhapsody/main.nf b/src/workflows/ingestion/bd_rhapsody/main.nf similarity index 98% rename from workflows/ingestion/bd_rhapsody/main.nf rename to src/workflows/ingestion/bd_rhapsody/main.nf index eaaebd80ac2..73db97e7858 100644 --- a/workflows/ingestion/bd_rhapsody/main.nf +++ b/src/workflows/ingestion/bd_rhapsody/main.nf @@ -1,6 +1,6 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { bd_rhapsody } from targetDir + "/mapping/bd_rhapsody/main.nf" diff --git a/workflows/multiomics/integration/bbknn_leiden/nextflow.config b/src/workflows/ingestion/bd_rhapsody/nextflow.config similarity index 57% rename from workflows/multiomics/integration/bbknn_leiden/nextflow.config rename to src/workflows/ingestion/bd_rhapsody/nextflow.config index 247e35cb80d..7fea8fb0abf 100644 --- a/workflows/multiomics/integration/bbknn_leiden/nextflow.config +++ b/src/workflows/ingestion/bd_rhapsody/nextflow.config @@ -7,5 +7,5 @@ params { } // include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") \ No newline at end of file +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/ingestion/cellranger_mapping/config.vsh.yaml b/src/workflows/ingestion/cellranger_mapping/config.vsh.yaml similarity index 98% rename from workflows/ingestion/cellranger_mapping/config.vsh.yaml rename to src/workflows/ingestion/cellranger_mapping/config.vsh.yaml index e0b99f46e64..28000d32037 100644 --- a/workflows/ingestion/cellranger_mapping/config.vsh.yaml +++ b/src/workflows/ingestion/cellranger_mapping/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "cellranger_mapping" - namespace: "ingestion" + namespace: "workflows/ingestion" description: "A pipeline for running Cell Ranger mapping." info: name: Cell Ranger mapping @@ -103,3 +103,5 @@ functionality: path: main.nf entrypoint: test_wf - path: /resources_test/cellranger_tiny_fastq +platforms: + - type: nextflow \ No newline at end of file diff --git a/workflows/ingestion/cellranger_mapping/integration_test.sh b/src/workflows/ingestion/cellranger_mapping/integration_test.sh similarity index 100% rename from workflows/ingestion/cellranger_mapping/integration_test.sh rename to src/workflows/ingestion/cellranger_mapping/integration_test.sh diff --git a/workflows/ingestion/cellranger_mapping/main.nf b/src/workflows/ingestion/cellranger_mapping/main.nf similarity index 98% rename from workflows/ingestion/cellranger_mapping/main.nf rename to src/workflows/ingestion/cellranger_mapping/main.nf index 7c648f59d04..d755fe4b2df 100644 --- a/workflows/ingestion/cellranger_mapping/main.nf +++ b/src/workflows/ingestion/cellranger_mapping/main.nf @@ -1,6 +1,6 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { cellranger_count } from targetDir + "/mapping/cellranger_count/main.nf" diff --git a/workflows/multiomics/integration/harmony_leiden/nextflow.config b/src/workflows/ingestion/cellranger_mapping/nextflow.config similarity index 57% rename from workflows/multiomics/integration/harmony_leiden/nextflow.config rename to src/workflows/ingestion/cellranger_mapping/nextflow.config index 247e35cb80d..7fea8fb0abf 100644 --- a/workflows/multiomics/integration/harmony_leiden/nextflow.config +++ b/src/workflows/ingestion/cellranger_mapping/nextflow.config @@ -7,5 +7,5 @@ params { } // include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") \ No newline at end of file +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/ingestion/cellranger_multi/config.vsh.yaml b/src/workflows/ingestion/cellranger_multi/config.vsh.yaml similarity index 98% rename from workflows/ingestion/cellranger_multi/config.vsh.yaml rename to src/workflows/ingestion/cellranger_multi/config.vsh.yaml index d54b3e593a4..b4554258b84 100644 --- a/workflows/ingestion/cellranger_multi/config.vsh.yaml +++ b/src/workflows/ingestion/cellranger_multi/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "cellranger_multi" - namespace: "ingestion" + namespace: "workflows/ingestion" description: "A pipeline for running Cell Ranger multi." info: name: Cell Ranger multi @@ -169,4 +169,6 @@ functionality: entrypoint: test_wf - path: /resources_test/10x_5k_anticmv/raw/ dest: 10x_5k_anticmv/raw/ - - path: /resources_test/reference_gencodev41_chr1 \ No newline at end of file + - path: /resources_test/reference_gencodev41_chr1 +platforms: + - type: nextflow \ No newline at end of file diff --git a/workflows/ingestion/cellranger_multi/integration_test.sh b/src/workflows/ingestion/cellranger_multi/integration_test.sh similarity index 100% rename from workflows/ingestion/cellranger_multi/integration_test.sh rename to src/workflows/ingestion/cellranger_multi/integration_test.sh diff --git a/workflows/ingestion/cellranger_multi/main.nf b/src/workflows/ingestion/cellranger_multi/main.nf similarity index 98% rename from workflows/ingestion/cellranger_multi/main.nf rename to src/workflows/ingestion/cellranger_multi/main.nf index 7b00cb75e1f..c4e21222c23 100644 --- a/workflows/ingestion/cellranger_multi/main.nf +++ b/src/workflows/ingestion/cellranger_multi/main.nf @@ -1,6 +1,6 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" diff --git a/workflows/multiomics/integration/initialize_integration/nextflow.config b/src/workflows/ingestion/cellranger_multi/nextflow.config similarity index 57% rename from workflows/multiomics/integration/initialize_integration/nextflow.config rename to src/workflows/ingestion/cellranger_multi/nextflow.config index 247e35cb80d..7fea8fb0abf 100644 --- a/workflows/multiomics/integration/initialize_integration/nextflow.config +++ b/src/workflows/ingestion/cellranger_multi/nextflow.config @@ -7,5 +7,5 @@ params { } // include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") \ No newline at end of file +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/ingestion/cellranger_postprocessing/config.vsh.yaml b/src/workflows/ingestion/cellranger_postprocessing/config.vsh.yaml similarity index 96% rename from workflows/ingestion/cellranger_postprocessing/config.vsh.yaml rename to src/workflows/ingestion/cellranger_postprocessing/config.vsh.yaml index c478017c242..cd090f1e3a6 100644 --- a/workflows/ingestion/cellranger_postprocessing/config.vsh.yaml +++ b/src/workflows/ingestion/cellranger_postprocessing/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "cellranger_postprocessing" - namespace: "ingestion" + namespace: "workflows/ingestion" description: "Post-processing Cell Ranger datasets." info: name: Cell Ranger post-processing @@ -60,3 +60,5 @@ functionality: entrypoint: test_wf2 - path: /resources_test/pbmc_1k_protein_v3 +platforms: + - type: nextflow diff --git a/workflows/ingestion/cellranger_postprocessing/integration_test.sh b/src/workflows/ingestion/cellranger_postprocessing/integration_test.sh similarity index 100% rename from workflows/ingestion/cellranger_postprocessing/integration_test.sh rename to src/workflows/ingestion/cellranger_postprocessing/integration_test.sh diff --git a/workflows/ingestion/cellranger_postprocessing/main.nf b/src/workflows/ingestion/cellranger_postprocessing/main.nf similarity index 99% rename from workflows/ingestion/cellranger_postprocessing/main.nf rename to src/workflows/ingestion/cellranger_postprocessing/main.nf index 49bdcef748a..0bf7a79350f 100644 --- a/workflows/ingestion/cellranger_postprocessing/main.nf +++ b/src/workflows/ingestion/cellranger_postprocessing/main.nf @@ -1,6 +1,6 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { cellbender_remove_background } from targetDir + "/correction/cellbender_remove_background/main.nf" diff --git a/workflows/multiomics/integration/scanorama_leiden/nextflow.config b/src/workflows/ingestion/cellranger_postprocessing/nextflow.config similarity index 57% rename from workflows/multiomics/integration/scanorama_leiden/nextflow.config rename to src/workflows/ingestion/cellranger_postprocessing/nextflow.config index 247e35cb80d..7fea8fb0abf 100644 --- a/workflows/multiomics/integration/scanorama_leiden/nextflow.config +++ b/src/workflows/ingestion/cellranger_postprocessing/nextflow.config @@ -7,5 +7,5 @@ params { } // include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") \ No newline at end of file +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/ingestion/conversion/config.vsh.yaml b/src/workflows/ingestion/conversion/config.vsh.yaml similarity index 96% rename from workflows/ingestion/conversion/config.vsh.yaml rename to src/workflows/ingestion/conversion/config.vsh.yaml index 83da8c6af6d..2fb2308f9ac 100644 --- a/workflows/ingestion/conversion/config.vsh.yaml +++ b/src/workflows/ingestion/conversion/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "conversion" - namespace: "ingestion" + namespace: "workflows/ingestion" description: "A pipeline to convert different file formats to .h5mu." authors: - __merge__: /src/authors/dries_schaumont.yaml @@ -52,4 +52,5 @@ functionality: path: main.nf entrypoint: test_wf - path: /resources_test/pbmc_1k_protein_v3 - +platforms: + - type: nextflow diff --git a/workflows/ingestion/conversion/integration_test.sh b/src/workflows/ingestion/conversion/integration_test.sh similarity index 100% rename from workflows/ingestion/conversion/integration_test.sh rename to src/workflows/ingestion/conversion/integration_test.sh diff --git a/workflows/ingestion/conversion/main.nf b/src/workflows/ingestion/conversion/main.nf similarity index 98% rename from workflows/ingestion/conversion/main.nf rename to src/workflows/ingestion/conversion/main.nf index 58e3b6c56fd..f84047b2bbd 100644 --- a/workflows/ingestion/conversion/main.nf +++ b/src/workflows/ingestion/conversion/main.nf @@ -1,6 +1,6 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { from_10xh5_to_h5mu } from targetDir + "/convert/from_10xh5_to_h5mu/main.nf" diff --git a/src/workflows/ingestion/conversion/nextflow.config b/src/workflows/ingestion/conversion/nextflow.config new file mode 100644 index 00000000000..9756b1dcc4f --- /dev/null +++ b/src/workflows/ingestion/conversion/nextflow.config @@ -0,0 +1,12 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() +} + + +// include common settings +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/ingestion/demux/config.vsh.yaml b/src/workflows/ingestion/demux/config.vsh.yaml similarity index 96% rename from workflows/ingestion/demux/config.vsh.yaml rename to src/workflows/ingestion/demux/config.vsh.yaml index 1461245b0b7..2022e948e3e 100644 --- a/workflows/ingestion/demux/config.vsh.yaml +++ b/src/workflows/ingestion/demux/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: demux - namespace: ingestion + namespace: workflows/ingestion description: | Convert `.bcl` files to `.fastq` files using bcl2fastq, bcl-convert or Cell Ranger mkfastq. info: @@ -52,3 +52,5 @@ functionality: path: main.nf entrypoint: test_wf - path: /resources_test/cellranger_tiny_bcl +platforms: + - type: nextflow \ No newline at end of file diff --git a/workflows/ingestion/demux/integration_test.sh b/src/workflows/ingestion/demux/integration_test.sh similarity index 100% rename from workflows/ingestion/demux/integration_test.sh rename to src/workflows/ingestion/demux/integration_test.sh diff --git a/workflows/ingestion/demux/main.nf b/src/workflows/ingestion/demux/main.nf similarity index 98% rename from workflows/ingestion/demux/main.nf rename to src/workflows/ingestion/demux/main.nf index cf9ccd25fd6..c6f95b1891b 100644 --- a/workflows/ingestion/demux/main.nf +++ b/src/workflows/ingestion/demux/main.nf @@ -1,6 +1,6 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { cellranger_mkfastq } from targetDir + "/demux/cellranger_mkfastq/main.nf" diff --git a/src/workflows/ingestion/demux/nextflow.config b/src/workflows/ingestion/demux/nextflow.config new file mode 100644 index 00000000000..92abc35e551 --- /dev/null +++ b/src/workflows/ingestion/demux/nextflow.config @@ -0,0 +1,11 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") diff --git a/workflows/ingestion/make_reference/config.vsh.yaml b/src/workflows/ingestion/make_reference/config.vsh.yaml similarity index 97% rename from workflows/ingestion/make_reference/config.vsh.yaml rename to src/workflows/ingestion/make_reference/config.vsh.yaml index f3b091c0f26..1d27328c0b9 100644 --- a/workflows/ingestion/make_reference/config.vsh.yaml +++ b/src/workflows/ingestion/make_reference/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: make_reference - namespace: ingestion + namespace: workflows/ingestion description: | Build a transcriptomics reference into one of many formats. authors: @@ -78,3 +78,5 @@ functionality: path: main.nf entrypoint: test_wf - path: /resources_test/reference_gencodev41_chr1 +platforms: + - type: nextflow \ No newline at end of file diff --git a/workflows/ingestion/make_reference/integration_test.sh b/src/workflows/ingestion/make_reference/integration_test.sh similarity index 100% rename from workflows/ingestion/make_reference/integration_test.sh rename to src/workflows/ingestion/make_reference/integration_test.sh diff --git a/workflows/ingestion/make_reference/main.nf b/src/workflows/ingestion/make_reference/main.nf similarity index 98% rename from workflows/ingestion/make_reference/main.nf rename to src/workflows/ingestion/make_reference/main.nf index 885f55b714a..8cbd6289330 100644 --- a/workflows/ingestion/make_reference/main.nf +++ b/src/workflows/ingestion/make_reference/main.nf @@ -1,6 +1,6 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { make_reference } from targetDir + "/reference/make_reference/main.nf" diff --git a/src/workflows/ingestion/make_reference/nextflow.config b/src/workflows/ingestion/make_reference/nextflow.config new file mode 100644 index 00000000000..92abc35e551 --- /dev/null +++ b/src/workflows/ingestion/make_reference/nextflow.config @@ -0,0 +1,11 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") diff --git a/workflows/test/integration_test.R b/src/workflows/integration_test.R similarity index 92% rename from workflows/test/integration_test.R rename to src/workflows/integration_test.R index 271fba4bbb2..be0c7c780ba 100644 --- a/workflows/test/integration_test.R +++ b/src/workflows/integration_test.R @@ -1,6 +1,6 @@ library(tidyverse) -workflows <- yaml::yaml.load(system("viash ns list -s workflows", intern = TRUE)) +workflows <- yaml::yaml.load(system("viash ns list -s src/workflows", intern = TRUE)) outs <- map_df(workflows, function(wf) { cat("Running ", wf$functionality$namespace, "/", wf$functionality$name, "\n", sep = "") @@ -29,7 +29,8 @@ outs <- map_df(workflows, function(wf) { "-main-script", paste0(dir, "/", test$path), "-entry", test$entrypoint, "-profile", "docker,no_publish", - "-with-dag", paste0(dir, "/graph.dot") + "-with-dag", paste0(dir, "/graph.dot"), + "-resume" ) start_time <- Sys.time() diff --git a/src/workflows/integration_test.sh b/src/workflows/integration_test.sh new file mode 100755 index 00000000000..05975872e68 --- /dev/null +++ b/src/workflows/integration_test.sh @@ -0,0 +1,5 @@ +#!/bin/bash + + + +Rscript src/workflows/integration_test.R | tee .viash_log_integration.txt \ No newline at end of file diff --git a/workflows/multiomics/full_pipeline/config.vsh.yaml b/src/workflows/multiomics/full_pipeline/config.vsh.yaml similarity index 99% rename from workflows/multiomics/full_pipeline/config.vsh.yaml rename to src/workflows/multiomics/full_pipeline/config.vsh.yaml index 0a78fc984e0..0a2a97314ee 100644 --- a/workflows/multiomics/full_pipeline/config.vsh.yaml +++ b/src/workflows/multiomics/full_pipeline/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "full_pipeline" - namespace: "multiomics" + namespace: "workflows/multiomics" description: "A pipeline to analyse multiple multiomics samples." authors: - __merge__: /src/authors/dries_schaumont.yaml @@ -196,3 +196,5 @@ functionality: # entrypoint: test_wf4 - path: /resources_test/concat_test_data - path: /resources_test/pbmc_1k_protein_v3 +platforms: + - type: nextflow diff --git a/workflows/multiomics/full_pipeline/integration_test.sh b/src/workflows/multiomics/full_pipeline/integration_test.sh similarity index 59% rename from workflows/multiomics/full_pipeline/integration_test.sh rename to src/workflows/multiomics/full_pipeline/integration_test.sh index 96bf91a87f3..9200269403e 100755 --- a/workflows/multiomics/full_pipeline/integration_test.sh +++ b/src/workflows/multiomics/full_pipeline/integration_test.sh @@ -12,52 +12,55 @@ export NXF_VER=21.10.6 nextflow \ run . \ - -main-script workflows/multiomics/full_pipeline/main.nf \ + -main-script src/workflows/multiomics/full_pipeline/main.nf \ -entry test_wf \ -resume \ -profile docker,no_publish \ - -c workflows/utils/labels_ci.config + -c src/workflows/utils/labels_ci.config # Same as above but with remote yaml file. nextflow \ run . \ - -main-script workflows/multiomics/full_pipeline/main.nf \ + -main-script src/workflows/multiomics/full_pipeline/main.nf \ + -entry test_wf \ -resume \ -profile docker,no_publish \ - -c workflows/utils/labels_ci.config \ + -c src/workflows/utils/labels_ci.config \ --param_list s3://openpipelines-data/remote_param_list/test_param_list.yaml # Same as above but with remote json file. nextflow \ run . \ - -main-script workflows/multiomics/full_pipeline/main.nf \ + -main-script src/workflows/multiomics/full_pipeline/main.nf \ + -entry test_wf \ -resume \ -profile docker,no_publish \ - -c workflows/utils/labels_ci.config \ + -c src/workflows/utils/labels_ci.config \ --param_list s3://openpipelines-data/remote_param_list/test_param_list.json # Same as above but with remote csv file. nextflow \ run . \ - -main-script workflows/multiomics/full_pipeline/main.nf \ + -main-script src/workflows/multiomics/full_pipeline/main.nf \ + -entry test_wf \ -resume \ -profile docker,no_publish \ - -c workflows/utils/labels_ci.config \ + -c src/workflows/utils/labels_ci.config \ --param_list s3://openpipelines-data/remote_param_list/test_param_list.csv nextflow \ run . \ - -main-script workflows/multiomics/full_pipeline/main.nf \ + -main-script src/workflows/multiomics/full_pipeline/main.nf \ -entry test_wf2 \ -resume \ -profile docker,no_publish \ - -c workflows/utils/labels_ci.config + -c src/workflows/utils/labels_ci.config nextflow \ run . \ - -main-script workflows/multiomics/full_pipeline/main.nf \ + -main-script src/workflows/multiomics/full_pipeline/main.nf \ -entry test_wf3 \ -resume \ -profile docker,no_publish \ - -c workflows/utils/labels_ci.config + -c src/workflows/utils/labels_ci.config diff --git a/workflows/multiomics/full_pipeline/main.nf b/src/workflows/multiomics/full_pipeline/main.nf similarity index 99% rename from workflows/multiomics/full_pipeline/main.nf rename to src/workflows/multiomics/full_pipeline/main.nf index 232f93d27b4..806ea7d6aee 100644 --- a/workflows/multiomics/full_pipeline/main.nf +++ b/src/workflows/multiomics/full_pipeline/main.nf @@ -1,5 +1,5 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { add_id } from targetDir + "/metadata/add_id/main.nf" diff --git a/src/workflows/multiomics/full_pipeline/nextflow.config b/src/workflows/multiomics/full_pipeline/nextflow.config new file mode 100644 index 00000000000..7fea8fb0abf --- /dev/null +++ b/src/workflows/multiomics/full_pipeline/nextflow.config @@ -0,0 +1,11 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/multiomics/full_pipeline/split_stub.nf b/src/workflows/multiomics/full_pipeline/split_stub.nf similarity index 100% rename from workflows/multiomics/full_pipeline/split_stub.nf rename to src/workflows/multiomics/full_pipeline/split_stub.nf diff --git a/workflows/multiomics/integration/bbknn_leiden/config.vsh.yaml b/src/workflows/multiomics/integration/bbknn_leiden/config.vsh.yaml similarity index 95% rename from workflows/multiomics/integration/bbknn_leiden/config.vsh.yaml rename to src/workflows/multiomics/integration/bbknn_leiden/config.vsh.yaml index 917891e1a99..ad4ddf481af 100644 --- a/workflows/multiomics/integration/bbknn_leiden/config.vsh.yaml +++ b/src/workflows/multiomics/integration/bbknn_leiden/config.vsh.yaml @@ -1,11 +1,11 @@ functionality: name: "bbknn_leiden" - namespace: "multiomics/integration" + namespace: "workflows/multiomics/integration" description: "Run bbknn followed by leiden clustering and run umap on the result." authors: - - __merge__: ../../../../src/authors/mauro_saporita.yaml + - __merge__: /src/authors/mauro_saporita.yaml roles: [ author ] - - __merge__: ../../../../src/authors/povilas_gibas.yaml + - __merge__: /src/authors/povilas_gibas.yaml roles: [ author ] argument_groups: - name: "Inputs" @@ -103,4 +103,6 @@ functionality: - type: nextflow_script path: main.nf entrypoint: test_wf2 - - path: /resources_test/pbmc_1k_protein_v3 \ No newline at end of file + - path: /resources_test/pbmc_1k_protein_v3 +platforms: + - type: nextflow \ No newline at end of file diff --git a/workflows/multiomics/integration/scvi_leiden/integration_test.sh b/src/workflows/multiomics/integration/bbknn_leiden/integration_test.sh similarity index 59% rename from workflows/multiomics/integration/scvi_leiden/integration_test.sh rename to src/workflows/multiomics/integration/bbknn_leiden/integration_test.sh index c4aad8c7bac..d75f29f36c9 100755 --- a/workflows/multiomics/integration/scvi_leiden/integration_test.sh +++ b/src/workflows/multiomics/integration/bbknn_leiden/integration_test.sh @@ -11,13 +11,13 @@ cd "$REPO_ROOT" export NXF_VER=21.10.6 nextflow run . \ - -main-script workflows/multiomics/integration/scvi_leiden/main.nf \ + -main-script src/workflows/multiomics/integration/bbknn_leiden/main.nf \ -profile docker,no_publish \ -entry test_wf \ - -c workflows/utils/labels_ci.config + -c src/workflows/utils/labels_ci.config nextflow run . \ - -main-script workflows/multiomics/integration/scvi_leiden/main.nf \ + -main-script src/workflows/multiomics/integration/bbknn_leiden/main.nf \ -profile docker,no_publish \ -entry test_wf2 \ - -c workflows/utils/labels_ci.config \ No newline at end of file + -c src/workflows/utils/labels_ci.config diff --git a/workflows/multiomics/integration/bbknn_leiden/main.nf b/src/workflows/multiomics/integration/bbknn_leiden/main.nf similarity index 99% rename from workflows/multiomics/integration/bbknn_leiden/main.nf rename to src/workflows/multiomics/integration/bbknn_leiden/main.nf index 9d208386675..5049f67f983 100644 --- a/workflows/multiomics/integration/bbknn_leiden/main.nf +++ b/src/workflows/multiomics/integration/bbknn_leiden/main.nf @@ -1,6 +1,6 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { leiden } from targetDir + '/cluster/leiden/main.nf' diff --git a/src/workflows/multiomics/integration/bbknn_leiden/nextflow.config b/src/workflows/multiomics/integration/bbknn_leiden/nextflow.config new file mode 100644 index 00000000000..21b717b00cb --- /dev/null +++ b/src/workflows/multiomics/integration/bbknn_leiden/nextflow.config @@ -0,0 +1,11 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/multiomics/integration/harmony_leiden/config.vsh.yaml b/src/workflows/multiomics/integration/harmony_leiden/config.vsh.yaml similarity index 97% rename from workflows/multiomics/integration/harmony_leiden/config.vsh.yaml rename to src/workflows/multiomics/integration/harmony_leiden/config.vsh.yaml index cf2f33dcbc5..08e7c0a3a2e 100644 --- a/workflows/multiomics/integration/harmony_leiden/config.vsh.yaml +++ b/src/workflows/multiomics/integration/harmony_leiden/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "harmony_leiden" - namespace: "multiomics/integration" + namespace: "workflows/multiomics/integration" description: "Run harmony integration followed by neighbour calculations, leiden clustering and run umap on the result." authors: - __merge__: /src/authors/dries_schaumont.yaml @@ -107,4 +107,6 @@ functionality: - type: nextflow_script path: main.nf entrypoint: test_wf2 - - path: /resources_test/pbmc_1k_protein_v3 \ No newline at end of file + - path: /resources_test/pbmc_1k_protein_v3 +platforms: + - type: nextflow \ No newline at end of file diff --git a/workflows/multiomics/integration/bbknn_leiden/integration_test.sh b/src/workflows/multiomics/integration/harmony_leiden/integration_test.sh similarity index 58% rename from workflows/multiomics/integration/bbknn_leiden/integration_test.sh rename to src/workflows/multiomics/integration/harmony_leiden/integration_test.sh index e3acae5de9f..5af21fe7d9d 100755 --- a/workflows/multiomics/integration/bbknn_leiden/integration_test.sh +++ b/src/workflows/multiomics/integration/harmony_leiden/integration_test.sh @@ -11,13 +11,14 @@ cd "$REPO_ROOT" export NXF_VER=21.10.6 nextflow run . \ - -main-script workflows/multiomics/integration/bbknn_leiden/main.nf \ + -main-script src/workflows/multiomics/integration/harmony_leiden/main.nf \ -profile docker,no_publish \ -entry test_wf \ - -c workflows/utils/labels_ci.config + -c src/workflows/utils/labels_ci.config nextflow run . \ - -main-script workflows/multiomics/integration/bbknn_leiden/main.nf \ + -main-script src/workflows/multiomics/integration/harmony_leiden/main.nf \ -profile docker,no_publish \ -entry test_wf2 \ - -c workflows/utils/labels_ci.config + -c src/workflows/utils/labels_ci.config + diff --git a/workflows/multiomics/integration/harmony_leiden/main.nf b/src/workflows/multiomics/integration/harmony_leiden/main.nf similarity index 99% rename from workflows/multiomics/integration/harmony_leiden/main.nf rename to src/workflows/multiomics/integration/harmony_leiden/main.nf index a5ddb4e6ec0..ff8668d46fa 100644 --- a/workflows/multiomics/integration/harmony_leiden/main.nf +++ b/src/workflows/multiomics/integration/harmony_leiden/main.nf @@ -1,7 +1,7 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { leiden } from targetDir + '/cluster/leiden/main.nf' diff --git a/src/workflows/multiomics/integration/harmony_leiden/nextflow.config b/src/workflows/multiomics/integration/harmony_leiden/nextflow.config new file mode 100644 index 00000000000..21b717b00cb --- /dev/null +++ b/src/workflows/multiomics/integration/harmony_leiden/nextflow.config @@ -0,0 +1,11 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/multiomics/integration/initialize_integration/config.vsh.yaml b/src/workflows/multiomics/integration/initialize_integration/config.vsh.yaml similarity index 95% rename from workflows/multiomics/integration/initialize_integration/config.vsh.yaml rename to src/workflows/multiomics/integration/initialize_integration/config.vsh.yaml index 85bc6cdb217..8c6eecef151 100644 --- a/workflows/multiomics/integration/initialize_integration/config.vsh.yaml +++ b/src/workflows/multiomics/integration/initialize_integration/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "initialize_integration" - namespace: "multiomics/integration" + namespace: "workflows/multiomics/integration" description: "Run calculations that output information required for most integration methods: PCA, nearest neighbour and UMAP." authors: - __merge__: /src/authors/dries_schaumont.yaml @@ -78,4 +78,6 @@ functionality: - type: nextflow_script path: main.nf entrypoint: test_wf - - path: ..//resources_test/concat_test_data \ No newline at end of file + - path: ..//resources_test/concat_test_data +platforms: + - type: nextflow \ No newline at end of file diff --git a/workflows/multiomics/integration/initialize_integration/integration_test.sh b/src/workflows/multiomics/integration/initialize_integration/integration_test.sh similarity index 64% rename from workflows/multiomics/integration/initialize_integration/integration_test.sh rename to src/workflows/multiomics/integration/initialize_integration/integration_test.sh index 181ee9fb7ee..2a5d83318c0 100755 --- a/workflows/multiomics/integration/initialize_integration/integration_test.sh +++ b/src/workflows/multiomics/integration/initialize_integration/integration_test.sh @@ -11,9 +11,9 @@ cd "$REPO_ROOT" export NXF_VER=21.10.6 nextflow run . \ - -main-script workflows/multiomics/integration/initialize_integration/main.nf \ + -main-script src/workflows/multiomics/integration/initialize_integration/main.nf \ -profile docker,no_publish \ -entry test_wf \ -with-trace work/trace.txt \ - -with-dag workflows/multiomics/integration/initialize_integration/graph.dot \ + -with-dag src/workflows/multiomics/integration/initialize_integration/graph.dot \ -resume \ No newline at end of file diff --git a/workflows/multiomics/integration/initialize_integration/main.nf b/src/workflows/multiomics/integration/initialize_integration/main.nf similarity index 98% rename from workflows/multiomics/integration/initialize_integration/main.nf rename to src/workflows/multiomics/integration/initialize_integration/main.nf index d361f073746..4a6691ce030 100644 --- a/workflows/multiomics/integration/initialize_integration/main.nf +++ b/src/workflows/multiomics/integration/initialize_integration/main.nf @@ -1,6 +1,6 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { pca } from targetDir + '/dimred/pca/main.nf' diff --git a/src/workflows/multiomics/integration/initialize_integration/nextflow.config b/src/workflows/multiomics/integration/initialize_integration/nextflow.config new file mode 100644 index 00000000000..21b717b00cb --- /dev/null +++ b/src/workflows/multiomics/integration/initialize_integration/nextflow.config @@ -0,0 +1,11 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/multiomics/integration/scanorama_leiden/config.vsh.yaml b/src/workflows/multiomics/integration/scanorama_leiden/config.vsh.yaml similarity index 98% rename from workflows/multiomics/integration/scanorama_leiden/config.vsh.yaml rename to src/workflows/multiomics/integration/scanorama_leiden/config.vsh.yaml index 36b39d5c8f3..373bd9cd7ba 100644 --- a/workflows/multiomics/integration/scanorama_leiden/config.vsh.yaml +++ b/src/workflows/multiomics/integration/scanorama_leiden/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "scanorama_leiden" - namespace: "multiomics/integration" + namespace: "workflows/multiomics/integration" description: "Run scanorama integration followed by neighbour calculations, leiden clustering and run umap on the result." authors: - __merge__: /src/authors/mauro_saporita.yaml @@ -120,3 +120,5 @@ functionality: path: main.nf entrypoint: test_wf2 - path: /resources_test/pbmc_1k_protein_v3 +platforms: + - type: nextflow diff --git a/workflows/multiomics/integration/scanorama_leiden/integration_test.sh b/src/workflows/multiomics/integration/scanorama_leiden/integration_test.sh similarity index 67% rename from workflows/multiomics/integration/scanorama_leiden/integration_test.sh rename to src/workflows/multiomics/integration/scanorama_leiden/integration_test.sh index f7fd13d1bd6..19bf3d67bae 100755 --- a/workflows/multiomics/integration/scanorama_leiden/integration_test.sh +++ b/src/workflows/multiomics/integration/scanorama_leiden/integration_test.sh @@ -11,11 +11,11 @@ cd "$REPO_ROOT" export NXF_VER=21.10.6 nextflow run . \ - -main-script workflows/multiomics/integration/scanorama_leiden/main.nf \ + -main-script src/workflows/multiomics/integration/scanorama_leiden/main.nf \ -profile docker,no_publish \ -entry test_wf nextflow run . \ - -main-script workflows/multiomics/integration/scanorama_leiden/main.nf \ + -main-script src/workflows/multiomics/integration/scanorama_leiden/main.nf \ -profile docker,no_publish \ -entry test_wf2 diff --git a/workflows/multiomics/integration/scanorama_leiden/main.nf b/src/workflows/multiomics/integration/scanorama_leiden/main.nf similarity index 99% rename from workflows/multiomics/integration/scanorama_leiden/main.nf rename to src/workflows/multiomics/integration/scanorama_leiden/main.nf index 9e835faa1ac..c35089ab117 100644 --- a/workflows/multiomics/integration/scanorama_leiden/main.nf +++ b/src/workflows/multiomics/integration/scanorama_leiden/main.nf @@ -1,6 +1,6 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { leiden } from targetDir + '/cluster/leiden/main.nf' diff --git a/src/workflows/multiomics/integration/scanorama_leiden/nextflow.config b/src/workflows/multiomics/integration/scanorama_leiden/nextflow.config new file mode 100644 index 00000000000..21b717b00cb --- /dev/null +++ b/src/workflows/multiomics/integration/scanorama_leiden/nextflow.config @@ -0,0 +1,11 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/multiomics/integration/scvi_leiden/config.vsh.yaml b/src/workflows/multiomics/integration/scvi_leiden/config.vsh.yaml similarity index 97% rename from workflows/multiomics/integration/scvi_leiden/config.vsh.yaml rename to src/workflows/multiomics/integration/scvi_leiden/config.vsh.yaml index 5885a9be329..674cb162f7e 100644 --- a/workflows/multiomics/integration/scvi_leiden/config.vsh.yaml +++ b/src/workflows/multiomics/integration/scvi_leiden/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "scvi_leiden" - namespace: "multiomics/integration" + namespace: "workflows/multiomics/integration" description: "Run scvi integration followed by neighbour calculations, leiden clustering and run umap on the result." authors: - __merge__: /src/authors/dries_schaumont.yaml @@ -141,4 +141,6 @@ functionality: - type: nextflow_script path: main.nf entrypoint: test_wf2 - - path: /resources_test/pbmc_1k_protein_v3 \ No newline at end of file + - path: /resources_test/pbmc_1k_protein_v3 +platforms: + - type: nextflow \ No newline at end of file diff --git a/workflows/multiomics/integration/harmony_leiden/integration_test.sh b/src/workflows/multiomics/integration/scvi_leiden/integration_test.sh similarity index 59% rename from workflows/multiomics/integration/harmony_leiden/integration_test.sh rename to src/workflows/multiomics/integration/scvi_leiden/integration_test.sh index 7f69581d925..0ebff86198e 100755 --- a/workflows/multiomics/integration/harmony_leiden/integration_test.sh +++ b/src/workflows/multiomics/integration/scvi_leiden/integration_test.sh @@ -11,14 +11,13 @@ cd "$REPO_ROOT" export NXF_VER=21.10.6 nextflow run . \ - -main-script workflows/multiomics/integration/harmony_leiden/main.nf \ + -main-script src/workflows/multiomics/integration/scvi_leiden/main.nf \ -profile docker,no_publish \ -entry test_wf \ - -c workflows/utils/labels_ci.config + -c src/workflows/utils/labels_ci.config nextflow run . \ - -main-script workflows/multiomics/integration/harmony_leiden/main.nf \ + -main-script src/workflows/multiomics/integration/scvi_leiden/main.nf \ -profile docker,no_publish \ -entry test_wf2 \ - -c workflows/utils/labels_ci.config - + -c src/workflows/utils/labels_ci.config \ No newline at end of file diff --git a/workflows/multiomics/integration/scvi_leiden/main.nf b/src/workflows/multiomics/integration/scvi_leiden/main.nf similarity index 99% rename from workflows/multiomics/integration/scvi_leiden/main.nf rename to src/workflows/multiomics/integration/scvi_leiden/main.nf index 1f433753402..91e5657fc6b 100644 --- a/workflows/multiomics/integration/scvi_leiden/main.nf +++ b/src/workflows/multiomics/integration/scvi_leiden/main.nf @@ -1,7 +1,7 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { leiden } from targetDir + '/cluster/leiden/main.nf' diff --git a/src/workflows/multiomics/integration/scvi_leiden/nextflow.config b/src/workflows/multiomics/integration/scvi_leiden/nextflow.config new file mode 100644 index 00000000000..21b717b00cb --- /dev/null +++ b/src/workflows/multiomics/integration/scvi_leiden/nextflow.config @@ -0,0 +1,11 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/multiomics/integration/totalvi_leiden/config.vsh.yaml b/src/workflows/multiomics/integration/totalvi_leiden/config.vsh.yaml similarity index 98% rename from workflows/multiomics/integration/totalvi_leiden/config.vsh.yaml rename to src/workflows/multiomics/integration/totalvi_leiden/config.vsh.yaml index 0ab29a319ae..14a7ad94d7e 100644 --- a/workflows/multiomics/integration/totalvi_leiden/config.vsh.yaml +++ b/src/workflows/multiomics/integration/totalvi_leiden/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "totalvi_leiden" - namespace: "multiomics/integration" + namespace: "workflows/multiomics/integration" description: "Run totalVI integration followed by neighbour calculations, leiden clustering and run umap on the result." authors: - __merge__: /src/authors/dries_schaumont.yaml @@ -186,3 +186,5 @@ functionality: path: main.nf entrypoint: test_wf2 - path: /resources_test/pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu +platforms: + - type: nextflow diff --git a/workflows/multiomics/integration/totalvi_leiden/integration_test.sh b/src/workflows/multiomics/integration/totalvi_leiden/integration_test.sh similarity index 58% rename from workflows/multiomics/integration/totalvi_leiden/integration_test.sh rename to src/workflows/multiomics/integration/totalvi_leiden/integration_test.sh index 47571dfd254..1065a4e4f12 100755 --- a/workflows/multiomics/integration/totalvi_leiden/integration_test.sh +++ b/src/workflows/multiomics/integration/totalvi_leiden/integration_test.sh @@ -11,13 +11,13 @@ cd "$REPO_ROOT" export NXF_VER=23.04.2 nextflow run . \ - -main-script workflows/multiomics/integration/totalvi_leiden/main.nf \ + -main-script src/workflows/multiomics/integration/totalvi_leiden/main.nf \ -profile docker,no_publish \ -entry test_wf \ - -c workflows/utils/labels_ci.config + -c src/workflows/utils/labels_ci.config nextflow run . \ - -main-script workflows/multiomics/integration/totalvi_leiden/main.nf \ + -main-script src/workflows/multiomics/integration/totalvi_leiden/main.nf \ -profile docker,no_publish \ -entry test_wf2 \ - -c workflows/utils/labels_ci.config + -c src/workflows/utils/labels_ci.config diff --git a/workflows/multiomics/integration/totalvi_leiden/main.nf b/src/workflows/multiomics/integration/totalvi_leiden/main.nf similarity index 99% rename from workflows/multiomics/integration/totalvi_leiden/main.nf rename to src/workflows/multiomics/integration/totalvi_leiden/main.nf index 5bd544ed813..5175ef9c11c 100644 --- a/workflows/multiomics/integration/totalvi_leiden/main.nf +++ b/src/workflows/multiomics/integration/totalvi_leiden/main.nf @@ -1,7 +1,7 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { leiden } from targetDir + '/cluster/leiden/main.nf' diff --git a/src/workflows/multiomics/integration/totalvi_leiden/nextflow.config b/src/workflows/multiomics/integration/totalvi_leiden/nextflow.config new file mode 100644 index 00000000000..21b717b00cb --- /dev/null +++ b/src/workflows/multiomics/integration/totalvi_leiden/nextflow.config @@ -0,0 +1,11 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/multiomics/multisample/config.vsh.yaml b/src/workflows/multiomics/multisample/config.vsh.yaml similarity index 98% rename from workflows/multiomics/multisample/config.vsh.yaml rename to src/workflows/multiomics/multisample/config.vsh.yaml index 33619e27b37..3f03a29b63b 100644 --- a/workflows/multiomics/multisample/config.vsh.yaml +++ b/src/workflows/multiomics/multisample/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "multisample" - namespace: "multiomics" + namespace: "workflows/multiomics" description: | This workflow serves as an entrypoint into the 'full_pipeline' in order to re-run the multisample processing and the integration setup. An input .h5mu file will @@ -87,4 +87,5 @@ functionality: entrypoint: test_wf2 - path: /resources_test/concat_test_data - path: /resources_test/10x_5k_anticmv - +platforms: + - type: nextflow diff --git a/workflows/multiomics/multisample/integration_test.sh b/src/workflows/multiomics/multisample/integration_test.sh similarity index 81% rename from workflows/multiomics/multisample/integration_test.sh rename to src/workflows/multiomics/multisample/integration_test.sh index 16bfbfef425..4413f1867d1 100755 --- a/workflows/multiomics/multisample/integration_test.sh +++ b/src/workflows/multiomics/multisample/integration_test.sh @@ -12,10 +12,10 @@ export NXF_VER=23.04.2 nextflow \ run . \ - -main-script workflows/multiomics/multisample/main.nf \ + -main-script src/workflows/multiomics/multisample/main.nf \ -entry test_wf \ -profile docker,no_publish \ - -c workflows/utils/labels_ci.config \ + -c src/workflows/utils/labels_ci.config \ -resume diff --git a/workflows/multiomics/multisample/main.nf b/src/workflows/multiomics/multisample/main.nf similarity index 99% rename from workflows/multiomics/multisample/main.nf rename to src/workflows/multiomics/multisample/main.nf index 1c545d1e5cd..b4cc2046de7 100644 --- a/workflows/multiomics/multisample/main.nf +++ b/src/workflows/multiomics/multisample/main.nf @@ -1,5 +1,5 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { merge } from targetDir + '/dataflow/merge/main.nf' diff --git a/src/workflows/multiomics/multisample/nextflow.config b/src/workflows/multiomics/multisample/nextflow.config new file mode 100644 index 00000000000..7fea8fb0abf --- /dev/null +++ b/src/workflows/multiomics/multisample/nextflow.config @@ -0,0 +1,11 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/multiomics/prot_multisample/config.vsh.yaml b/src/workflows/multiomics/prot_multisample/config.vsh.yaml similarity index 94% rename from workflows/multiomics/prot_multisample/config.vsh.yaml rename to src/workflows/multiomics/prot_multisample/config.vsh.yaml index 865c8b4f0b9..a1c5be7460f 100644 --- a/workflows/multiomics/prot_multisample/config.vsh.yaml +++ b/src/workflows/multiomics/prot_multisample/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "prot_multisample" - namespace: "multiomics" + namespace: "workflows/multiomics" description: "Processing unimodal multi-sample ADT data." info: image: /images/concepts/fig_workflow_multiomics_adt_multisample.svg @@ -59,4 +59,6 @@ functionality: - type: nextflow_script path: main.nf entrypoint: test_wf - - path: /resources_test/pbmc_1k_protein_v3 \ No newline at end of file + - path: /resources_test/pbmc_1k_protein_v3 +platforms: + - type: nextflow \ No newline at end of file diff --git a/workflows/multiomics/prot_multisample/integration_test.sh b/src/workflows/multiomics/prot_multisample/integration_test.sh similarity index 81% rename from workflows/multiomics/prot_multisample/integration_test.sh rename to src/workflows/multiomics/prot_multisample/integration_test.sh index eb0274e7bcb..b69b9d6b833 100755 --- a/workflows/multiomics/prot_multisample/integration_test.sh +++ b/src/workflows/multiomics/prot_multisample/integration_test.sh @@ -9,7 +9,7 @@ cd "$REPO_ROOT" export NXF_VER=21.10.6 nextflow run . \ - -main-script workflows/multiomics/prot_multisample/main.nf \ + -main-script src/workflows/multiomics/prot_multisample/main.nf \ -profile docker,no_publish \ -entry test_wf \ -with-trace work/trace.txt \ No newline at end of file diff --git a/workflows/multiomics/prot_multisample/main.nf b/src/workflows/multiomics/prot_multisample/main.nf similarity index 98% rename from workflows/multiomics/prot_multisample/main.nf rename to src/workflows/multiomics/prot_multisample/main.nf index 9603371e437..53bf44b8c5e 100644 --- a/workflows/multiomics/prot_multisample/main.nf +++ b/src/workflows/multiomics/prot_multisample/main.nf @@ -1,6 +1,6 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { clr } from targetDir + '/transform/clr/main.nf' diff --git a/src/workflows/multiomics/prot_multisample/nextflow.config b/src/workflows/multiomics/prot_multisample/nextflow.config new file mode 100644 index 00000000000..7fea8fb0abf --- /dev/null +++ b/src/workflows/multiomics/prot_multisample/nextflow.config @@ -0,0 +1,11 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/multiomics/prot_singlesample/config.vsh.yaml b/src/workflows/multiomics/prot_singlesample/config.vsh.yaml similarity index 94% rename from workflows/multiomics/prot_singlesample/config.vsh.yaml rename to src/workflows/multiomics/prot_singlesample/config.vsh.yaml index f4cc0f7b809..90ae69b2793 100644 --- a/workflows/multiomics/prot_singlesample/config.vsh.yaml +++ b/src/workflows/multiomics/prot_singlesample/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "prot_singlesample" - namespace: "multiomics" + namespace: "workflows/multiomics" description: "Processing unimodal single-sample CITE-seq data." info: image: /images/concepts/fig_workflow_multiomics_adt_singlesample.svg @@ -64,4 +64,6 @@ functionality: - type: nextflow_script path: main.nf entrypoint: test_wf - - path: /resources_test/pbmc_1k_protein_v3 \ No newline at end of file + - path: /resources_test/pbmc_1k_protein_v3 +platforms: + - type: nextflow \ No newline at end of file diff --git a/workflows/multiomics/prot_singlesample/integration_test.sh b/src/workflows/multiomics/prot_singlesample/integration_test.sh similarity index 81% rename from workflows/multiomics/prot_singlesample/integration_test.sh rename to src/workflows/multiomics/prot_singlesample/integration_test.sh index f9eba6059f4..c2ee70c0660 100755 --- a/workflows/multiomics/prot_singlesample/integration_test.sh +++ b/src/workflows/multiomics/prot_singlesample/integration_test.sh @@ -9,7 +9,7 @@ cd "$REPO_ROOT" export NXF_VER=21.10.6 nextflow run . \ - -main-script workflows/multiomics/prot_singlesample/main.nf \ + -main-script src/workflows/multiomics/prot_singlesample/main.nf \ -profile docker,no_publish \ -resume \ -entry test_wf \ diff --git a/workflows/multiomics/prot_singlesample/main.nf b/src/workflows/multiomics/prot_singlesample/main.nf similarity index 98% rename from workflows/multiomics/prot_singlesample/main.nf rename to src/workflows/multiomics/prot_singlesample/main.nf index 50e39cb36cd..3a58830e6e1 100644 --- a/workflows/multiomics/prot_singlesample/main.nf +++ b/src/workflows/multiomics/prot_singlesample/main.nf @@ -1,6 +1,6 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { readConfig; helpMessage; channelFromParams; preprocessInputs } from workflowDir + "/utils/WorkflowHelper.nf" diff --git a/src/workflows/multiomics/prot_singlesample/nextflow.config b/src/workflows/multiomics/prot_singlesample/nextflow.config new file mode 100644 index 00000000000..7fea8fb0abf --- /dev/null +++ b/src/workflows/multiomics/prot_singlesample/nextflow.config @@ -0,0 +1,11 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/multiomics/rna_multisample/config.vsh.yaml b/src/workflows/multiomics/rna_multisample/config.vsh.yaml similarity index 98% rename from workflows/multiomics/rna_multisample/config.vsh.yaml rename to src/workflows/multiomics/rna_multisample/config.vsh.yaml index b02a5809369..c1c6e7a1293 100644 --- a/workflows/multiomics/rna_multisample/config.vsh.yaml +++ b/src/workflows/multiomics/rna_multisample/config.vsh.yaml @@ -91,4 +91,6 @@ functionality: - type: nextflow_script path: main.nf entrypoint: test_wf - - path: /resources_test/concat_test_data \ No newline at end of file + - path: /resources_test/concat_test_data +platforms: + - type: nextflow \ No newline at end of file diff --git a/workflows/multiomics/rna_multisample/integration_test.sh b/src/workflows/multiomics/rna_multisample/integration_test.sh similarity index 74% rename from workflows/multiomics/rna_multisample/integration_test.sh rename to src/workflows/multiomics/rna_multisample/integration_test.sh index 7d84816d8dc..e144fc1a6d9 100755 --- a/workflows/multiomics/rna_multisample/integration_test.sh +++ b/src/workflows/multiomics/rna_multisample/integration_test.sh @@ -11,9 +11,9 @@ cd "$REPO_ROOT" export NXF_VER=21.10.6 nextflow run . \ - -main-script workflows/multiomics/rna_multisample/main.nf \ + -main-script src/workflows/multiomics/rna_multisample/main.nf \ -profile docker,no_publish \ -resume \ -entry test_wf \ -with-trace work/trace.txt \ - -c workflows/utils/labels_ci.config + -c src/workflows/utils/labels_ci.config diff --git a/workflows/multiomics/rna_multisample/main.nf b/src/workflows/multiomics/rna_multisample/main.nf similarity index 98% rename from workflows/multiomics/rna_multisample/main.nf rename to src/workflows/multiomics/rna_multisample/main.nf index 749e93f2a1f..f740a85b4a6 100644 --- a/workflows/multiomics/rna_multisample/main.nf +++ b/src/workflows/multiomics/rna_multisample/main.nf @@ -1,6 +1,6 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { normalize_total } from targetDir + '/transform/normalize_total/main.nf' diff --git a/src/workflows/multiomics/rna_multisample/nextflow.config b/src/workflows/multiomics/rna_multisample/nextflow.config new file mode 100644 index 00000000000..7fea8fb0abf --- /dev/null +++ b/src/workflows/multiomics/rna_multisample/nextflow.config @@ -0,0 +1,11 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/multiomics/rna_singlesample/config.vsh.yaml b/src/workflows/multiomics/rna_singlesample/config.vsh.yaml similarity index 97% rename from workflows/multiomics/rna_singlesample/config.vsh.yaml rename to src/workflows/multiomics/rna_singlesample/config.vsh.yaml index 50bfc4a9d24..53d57baa8d6 100644 --- a/workflows/multiomics/rna_singlesample/config.vsh.yaml +++ b/src/workflows/multiomics/rna_singlesample/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "rna_singlesample" - namespace: "multiomics" + namespace: "workflows/multiomics" description: "Processing unimodal single-sample RNA transcriptomics data." info: image: /images/concepts/fig_workflow_multiomics_rna_singlesample.svg @@ -109,4 +109,6 @@ functionality: - type: nextflow_script path: main.nf entrypoint: test_wf - - path: /resources_test/pbmc_1k_protein_v3 \ No newline at end of file + - path: /resources_test/pbmc_1k_protein_v3 +platforms: + - type: nextflow \ No newline at end of file diff --git a/workflows/multiomics/rna_singlesample/integration_test.sh b/src/workflows/multiomics/rna_singlesample/integration_test.sh similarity index 88% rename from workflows/multiomics/rna_singlesample/integration_test.sh rename to src/workflows/multiomics/rna_singlesample/integration_test.sh index 025c3cee2e2..29a78bbaa42 100755 --- a/workflows/multiomics/rna_singlesample/integration_test.sh +++ b/src/workflows/multiomics/rna_singlesample/integration_test.sh @@ -11,7 +11,7 @@ cd "$REPO_ROOT" export NXF_VER=21.10.6 nextflow run . \ - -main-script workflows/multiomics/rna_singlesample/main.nf \ + -main-script src/workflows/multiomics/rna_singlesample/main.nf \ -profile docker,no_publish \ -entry test_wf \ -with-trace work/trace.txt \ diff --git a/workflows/multiomics/rna_singlesample/main.nf b/src/workflows/multiomics/rna_singlesample/main.nf similarity index 99% rename from workflows/multiomics/rna_singlesample/main.nf rename to src/workflows/multiomics/rna_singlesample/main.nf index 4f35d345350..3b994a30162 100644 --- a/workflows/multiomics/rna_singlesample/main.nf +++ b/src/workflows/multiomics/rna_singlesample/main.nf @@ -1,6 +1,6 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { filter_with_counts } from targetDir + "/filter/filter_with_counts/main.nf" diff --git a/src/workflows/multiomics/rna_singlesample/nextflow.config b/src/workflows/multiomics/rna_singlesample/nextflow.config new file mode 100644 index 00000000000..7fea8fb0abf --- /dev/null +++ b/src/workflows/multiomics/rna_singlesample/nextflow.config @@ -0,0 +1,11 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/qc/qc/config.vsh.yaml b/src/workflows/qc/qc/config.vsh.yaml similarity index 98% rename from workflows/qc/qc/config.vsh.yaml rename to src/workflows/qc/qc/config.vsh.yaml index 1d956c2da51..e47934bd752 100644 --- a/workflows/qc/qc/config.vsh.yaml +++ b/src/workflows/qc/qc/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "qc" - namespace: "qc" + namespace: "workflows/qc/qc" description: "A pipeline to add basic qc statistics to a MuData " authors: - __merge__: /src/authors/dries_schaumont.yaml @@ -97,3 +97,5 @@ functionality: entrypoint: test_wf - path: /resources_test/concat_test_data - path: /resources_test/pbmc_1k_protein_v3 +platforms: + - type: nextflow diff --git a/workflows/qc/qc/integration_test.sh b/src/workflows/qc/qc/integration_test.sh similarity index 76% rename from workflows/qc/qc/integration_test.sh rename to src/workflows/qc/qc/integration_test.sh index 4544b81def2..80f1e24246b 100755 --- a/workflows/qc/qc/integration_test.sh +++ b/src/workflows/qc/qc/integration_test.sh @@ -12,8 +12,8 @@ export NXF_VER=21.10.6 nextflow \ run . \ - -main-script workflows/qc/qc/main.nf \ + -main-script src/workflows/qc/qc/main.nf \ -entry test_wf \ -resume \ -profile docker,no_publish \ - -c workflows/utils/labels_ci.config + -c src/workflows/utils/labels_ci.config diff --git a/workflows/qc/qc/main.nf b/src/workflows/qc/qc/main.nf similarity index 99% rename from workflows/qc/qc/main.nf rename to src/workflows/qc/qc/main.nf index eb9222acaa8..b306626569b 100644 --- a/workflows/qc/qc/main.nf +++ b/src/workflows/qc/qc/main.nf @@ -1,5 +1,5 @@ nextflow.enable.dsl=2 -workflowDir = params.rootDir + "/workflows" +workflowDir = params.rootDir + "/src/workflows" targetDir = params.rootDir + "/target/nextflow" include { publish } from targetDir + '/transfer/publish/main.nf' diff --git a/src/workflows/qc/qc/nextflow.config b/src/workflows/qc/qc/nextflow.config new file mode 100644 index 00000000000..7fea8fb0abf --- /dev/null +++ b/src/workflows/qc/qc/nextflow.config @@ -0,0 +1,11 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/utils/DataflowHelper.nf b/src/workflows/utils/DataflowHelper.nf similarity index 100% rename from workflows/utils/DataflowHelper.nf rename to src/workflows/utils/DataflowHelper.nf diff --git a/workflows/utils/ProfilesHelper.config b/src/workflows/utils/ProfilesHelper.config similarity index 100% rename from workflows/utils/ProfilesHelper.config rename to src/workflows/utils/ProfilesHelper.config diff --git a/workflows/utils/WorkflowHelper.nf b/src/workflows/utils/WorkflowHelper.nf similarity index 100% rename from workflows/utils/WorkflowHelper.nf rename to src/workflows/utils/WorkflowHelper.nf diff --git a/workflows/utils/errorstrat_ignore.config b/src/workflows/utils/errorstrat_ignore.config similarity index 100% rename from workflows/utils/errorstrat_ignore.config rename to src/workflows/utils/errorstrat_ignore.config diff --git a/workflows/utils/labels.config b/src/workflows/utils/labels.config similarity index 100% rename from workflows/utils/labels.config rename to src/workflows/utils/labels.config diff --git a/workflows/utils/labels_ci.config b/src/workflows/utils/labels_ci.config similarity index 100% rename from workflows/utils/labels_ci.config rename to src/workflows/utils/labels_ci.config diff --git a/workflows/ingestion/bd_rhapsody/nextflow.config b/workflows/ingestion/bd_rhapsody/nextflow.config deleted file mode 100644 index 3c22aaf9b61..00000000000 --- a/workflows/ingestion/bd_rhapsody/nextflow.config +++ /dev/null @@ -1,11 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/ingestion/cellranger_mapping/nextflow.config b/workflows/ingestion/cellranger_mapping/nextflow.config deleted file mode 100644 index 3c22aaf9b61..00000000000 --- a/workflows/ingestion/cellranger_mapping/nextflow.config +++ /dev/null @@ -1,11 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/ingestion/cellranger_multi/nextflow.config b/workflows/ingestion/cellranger_multi/nextflow.config deleted file mode 100644 index 3c22aaf9b61..00000000000 --- a/workflows/ingestion/cellranger_multi/nextflow.config +++ /dev/null @@ -1,11 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/ingestion/cellranger_postprocessing/nextflow.config b/workflows/ingestion/cellranger_postprocessing/nextflow.config deleted file mode 100644 index 3c22aaf9b61..00000000000 --- a/workflows/ingestion/cellranger_postprocessing/nextflow.config +++ /dev/null @@ -1,11 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/ingestion/conversion/nextflow.config b/workflows/ingestion/conversion/nextflow.config deleted file mode 100644 index 7dcb45361b4..00000000000 --- a/workflows/ingestion/conversion/nextflow.config +++ /dev/null @@ -1,12 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() -} - - -// include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/ingestion/demux/nextflow.config b/workflows/ingestion/demux/nextflow.config deleted file mode 100644 index 425fb92fede..00000000000 --- a/workflows/ingestion/demux/nextflow.config +++ /dev/null @@ -1,11 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") diff --git a/workflows/ingestion/make_reference/nextflow.config b/workflows/ingestion/make_reference/nextflow.config deleted file mode 100644 index 425fb92fede..00000000000 --- a/workflows/ingestion/make_reference/nextflow.config +++ /dev/null @@ -1,11 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") diff --git a/workflows/multiomics/full_pipeline/nextflow.config b/workflows/multiomics/full_pipeline/nextflow.config deleted file mode 100644 index 3c22aaf9b61..00000000000 --- a/workflows/multiomics/full_pipeline/nextflow.config +++ /dev/null @@ -1,11 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/multiomics/integration/scvi_leiden/nextflow.config b/workflows/multiomics/integration/scvi_leiden/nextflow.config deleted file mode 100644 index 247e35cb80d..00000000000 --- a/workflows/multiomics/integration/scvi_leiden/nextflow.config +++ /dev/null @@ -1,11 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/multiomics/integration/totalvi_leiden/nextflow.config b/workflows/multiomics/integration/totalvi_leiden/nextflow.config deleted file mode 100644 index 247e35cb80d..00000000000 --- a/workflows/multiomics/integration/totalvi_leiden/nextflow.config +++ /dev/null @@ -1,11 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/multiomics/multisample/nextflow.config b/workflows/multiomics/multisample/nextflow.config deleted file mode 100644 index 3c22aaf9b61..00000000000 --- a/workflows/multiomics/multisample/nextflow.config +++ /dev/null @@ -1,11 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/multiomics/prot_multisample/nextflow.config b/workflows/multiomics/prot_multisample/nextflow.config deleted file mode 100644 index 3c22aaf9b61..00000000000 --- a/workflows/multiomics/prot_multisample/nextflow.config +++ /dev/null @@ -1,11 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/multiomics/prot_singlesample/nextflow.config b/workflows/multiomics/prot_singlesample/nextflow.config deleted file mode 100644 index 3c22aaf9b61..00000000000 --- a/workflows/multiomics/prot_singlesample/nextflow.config +++ /dev/null @@ -1,11 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/multiomics/rna_multisample/nextflow.config b/workflows/multiomics/rna_multisample/nextflow.config deleted file mode 100644 index 3c22aaf9b61..00000000000 --- a/workflows/multiomics/rna_multisample/nextflow.config +++ /dev/null @@ -1,11 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/multiomics/rna_singlesample/nextflow.config b/workflows/multiomics/rna_singlesample/nextflow.config deleted file mode 100644 index 3c22aaf9b61..00000000000 --- a/workflows/multiomics/rna_singlesample/nextflow.config +++ /dev/null @@ -1,11 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/qc/qc/nextflow.config b/workflows/qc/qc/nextflow.config deleted file mode 100644 index 3c22aaf9b61..00000000000 --- a/workflows/qc/qc/nextflow.config +++ /dev/null @@ -1,11 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") \ No newline at end of file diff --git a/workflows/test/integration_test.sh b/workflows/test/integration_test.sh deleted file mode 100755 index 94a93611072..00000000000 --- a/workflows/test/integration_test.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash - - - -Rscript workflows/test/integration_test.R | tee .viash_log_integration.txt \ No newline at end of file