Remove workflows folder.

.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: |

.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

.github/workflows/main-build-viash-hub.yml

@@ -39,19 +39,20 @@ 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'
 
     - 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: |

.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: |

.github/workflows/release-build-viash-hub.yml

@@ -49,19 +49,21 @@ 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'
 
     - 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

.github/workflows/release-build.yml

@@ -40,19 +40,20 @@ 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'
 
     - 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

.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

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

workflows/resources_test_scripts/10x_5k_anticmv.sh → 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"

workflows/resources_test_scripts/10x_5k_lung_crispr.sh → 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 
+  -c src/workflows/utils/labels.config 

workflows/resources_test_scripts/bdrhap_5kjrt.sh → 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

workflows/resources_test_scripts/bdrhap_vdj.sh → 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
+  -c src/workflows/utils/labels.config \
+  -c src/workflows/utils/errorstrat_ignore.config

workflows/resources_test_scripts/pbmc_1k_protein_v3.sh → 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" \

workflows/resources_test_scripts/ref_gencodev41_chr1.sh → 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" \

workflows/ingestion/bd_rhapsody/config.vsh.yaml → 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/
+    - path: /resources_test/reference_gencodev41_chr1/
+platforms:
+  - type: nextflow

workflows/ingestion/bd_rhapsody/main.nf → 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"

workflows/multiomics/integration/bbknn_leiden/nextflow.config → 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")
+includeConfig("${params.rootDir}/src/workflows/utils/ProfilesHelper.config")
+includeConfig("${params.rootDir}/src/workflows/utils/labels.config")

workflows/ingestion/cellranger_mapping/config.vsh.yaml → 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

workflows/ingestion/cellranger_mapping/main.nf → 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"