Merge pull request #1206 from nf-core/config_refactor

Remove lib directory and modules.config
nf-core · Feb 5, 2024 · a53a004 · a53a004
2 parents 07d7543 + aeec5a9
commit a53a004
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -35,38 +35,9 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Hash Github Workspace
-        id: hash_workspace
-        run: |
-          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
-
-      - name: Cache test data
-        id: cache-testdata
-        uses: actions/cache@v3
-        with:
-          path: test-datasets/
-          key: ${{ steps.hash_workspace.outputs.digest }}
-
-      - name: Check out test data
-        if: steps.cache-testdata.outputs.cache-hit != 'true'
-        uses: actions/checkout@v3
-        with:
-          repository: nf-core/test-datasets
-          ref: rnaseq3
-          path: test-datasets/
-
-      - name: Replace remote paths in samplesheets
-        run: |
-          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
-            echo "========== $f ============"
-            cat $f
-            echo "========================================"
-          done;
-
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
 
   star_salmon:
     name: Test STAR Salmon with workflow parameters
@@ -92,43 +63,14 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
-      - name: Hash Github Workspace
-        id: hash_workspace
-        run: |
-          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
-
-      - name: Cache test data
-        id: cache-testdata
-        uses: actions/cache@v3
-        with:
-          path: test-datasets/
-          key: ${{ steps.hash_workspace.outputs.digest }}
-
-      - name: Check out test data
-        if: steps.cache-testdata.outputs.cache-hit != 'true'
-        uses: actions/checkout@v3
-        with:
-          repository: nf-core/test-datasets
-          ref: rnaseq3
-          path: test-datasets/
-
-      - name: Replace remote paths in samplesheets
-        run: |
-          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
-            echo "========== $f ============"
-            cat $f
-            echo "========================================"
-          done;
-
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
       - name: Run pipeline with STAR and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results
 
   star_rsem:
     name: Test STAR RSEM with workflow parameters
@@ -143,43 +85,14 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
-      - name: Hash Github Workspace
-        id: hash_workspace
-        run: |
-          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
-
-      - name: Cache test data
-        id: cache-testdata
-        uses: actions/cache@v3
-        with:
-          path: test-datasets/
-          key: ${{ steps.hash_workspace.outputs.digest }}
-
-      - name: Check out test data
-        if: steps.cache-testdata.outputs.cache-hit != 'true'
-        uses: actions/checkout@v3
-        with:
-          repository: nf-core/test-datasets
-          ref: rnaseq3
-          path: test-datasets/
-
-      - name: Replace remote paths in samplesheets
-        run: |
-          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
-            echo "========== $f ============"
-            cat $f
-            echo "========================================"
-          done;
-
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
       - name: Run pipeline with RSEM STAR and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results
 
   hisat2:
     name: Test HISAT2 with workflow parameters
@@ -194,43 +107,14 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
-      - name: Hash Github Workspace
-        id: hash_workspace
-        run: |
-          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
-
-      - name: Cache test data
-        id: cache-testdata
-        uses: actions/cache@v3
-        with:
-          path: test-datasets/
-          key: ${{ steps.hash_workspace.outputs.digest }}
-
-      - name: Check out test data
-        if: steps.cache-testdata.outputs.cache-hit != 'true'
-        uses: actions/checkout@v3
-        with:
-          repository: nf-core/test-datasets
-          ref: rnaseq3
-          path: test-datasets/
-
-      - name: Replace remote paths in samplesheets
-        run: |
-          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
-            echo "========== $f ============"
-            cat $f
-            echo "========================================"
-          done;
-
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
       - name: Run pipeline with HISAT2 and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results
 
   pseudo:
     name: Test Pseudoaligners with workflow parameters
@@ -249,40 +133,11 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
-      - name: Hash Github Workspace
-        id: hash_workspace
-        run: |
-          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
-
-      - name: Cache test data
-        id: cache-testdata
-        uses: actions/cache@v3
-        with:
-          path: test-datasets/
-          key: ${{ steps.hash_workspace.outputs.digest }}
-
-      - name: Check out test data
-        if: steps.cache-testdata.outputs.cache-hit != 'true'
-        uses: actions/checkout@v3
-        with:
-          repository: nf-core/test-datasets
-          ref: rnaseq3
-          path: test-datasets/
-
-      - name: Replace remote paths in samplesheets
-        run: |
-          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
-            echo "========== $f ============"
-            cat $f
-            echo "========================================"
-          done;
-
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
       - name: Run pipeline with Salmon or Kallisto and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }} --outdir ./results
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -3,7 +3,11 @@ lint:
   files_unchanged:
     - assets/email_template.html
     - assets/email_template.txt
+  files_exist:
+    - conf/modules.config
     - lib/NfcoreTemplate.groovy
+    - lib/Utils.groovy
+    - lib/WorkflowMain.groovy
   nextflow_config:
     - config_defaults:
         - params.ribo_database_manifest
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [PR #1186](https://github.com/nf-core/rnaseq/pull/1186) - Properly update qualimap/rnaseq module (ie not patch)
 - [PR #1201](https://github.com/nf-core/rnaseq/pull/1201) - Template update for nf-core/tools v2.12
+- [PR #1206](https://github.com/nf-core/rnaseq/pull/1206) - Remove `lib/` directory and `modules.config`
 
 ### Parameters
 

diff --git a/assets/dummy_file.txt b/assets/dummy_file.txt
diff --git a/conf/base.config b/conf/base.config
@@ -57,7 +57,4 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
 }