Merge pull request #388 from ypriverol/dev

Update sdrf-pipelines 0.0.26 -> 0.0.27
bigbio · Jul 17, 2024 · 94424c4 · 94424c4
2 parents c4e35a2 + d4d0d1f
commit 94424c4
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Showing 4 changed files with 14 additions and 10 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -56,12 +56,14 @@ jobs:
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: Install micromamba
+        env:
+          MAMBA_ROOT_PREFIX: ${{ github.workspace }}/.micromamba
         if: matrix.exec_profile == 'conda'
         run: |
           wget -qO- https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
           echo "$(pwd)/bin" >> $GITHUB_PATH
           echo "$(pwd)/micromamba/bin" >> $GITHUB_PATH
-          ./bin/micromamba shell init -s bash -p ./micromamba
+          ./bin/micromamba shell init -s bash
           echo $'channels:\n  - conda-forge\n  - bioconda\n  - defaults\nuse_lockfiles: false' >> ~/.mambarc
 
       - name: Run pipeline with test data
@@ -72,6 +74,8 @@ jobs:
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results
       - name: Run pipeline with test data in conda profile (and single-threaded)
+        env:
+          MAMBA_ROOT_PREFIX: ${{ github.workspace }}/.micromamba
         if: matrix.exec_profile == 'conda'
         # TODO nf-core: You can customise CI pipeline run tests as required
         # For example: adding multiple test runs with different parameters

diff --git a/modules/local/preprocess_expdesign.nf b/modules/local/preprocess_expdesign.nf
@@ -6,11 +6,11 @@ process PREPROCESS_EXPDESIGN {
     tag "$design.Name"
     label 'process_low'
 
-    conda "bioconda::sdrf-pipelines=0.0.26"
+    conda "bioconda::sdrf-pipelines=0.0.27"
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.26--pyhdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.27--pyhdfd78af_0"
     } else {
-        container "biocontainers/sdrf-pipelines:0.0.26--pyhdfd78af_0"
+        container "biocontainers/sdrf-pipelines:0.0.27--pyhdfd78af_0"
     }
 
     input:

diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
@@ -3,11 +3,11 @@ process SAMPLESHEET_CHECK {
     tag "$input_file"
     label 'process_single'
 
-    conda "bioconda::sdrf-pipelines=0.0.26"
+    conda "bioconda::sdrf-pipelines=0.0.27"
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.26--pyhdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.27--pyhdfd78af_0"
     } else {
-        container "biocontainers/sdrf-pipelines:0.0.26--pyhdfd78af_0"
+        container "biocontainers/sdrf-pipelines:0.0.27--pyhdfd78af_0"
     }
 
     input:

diff --git a/modules/local/sdrfparsing/main.nf b/modules/local/sdrfparsing/main.nf
@@ -2,10 +2,10 @@ process SDRFPARSING {
     tag "$sdrf.Name"
     label 'process_low'
 
-    conda "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.26"
+    conda "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.27"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.26--pyhdfd78af_0' :
-        'biocontainers/sdrf-pipelines:0.0.26--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.27--pyhdfd78af_0' :
+        'biocontainers/sdrf-pipelines:0.0.27--pyhdfd78af_0' }"
 
     input:
     path sdrf