style: Add back in container elvis operator

nf-core · Jun 18, 2024 · 4bb75f8 · 4bb75f8
1 parent 825f86a
commit 4bb75f8
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Showing 7 changed files with 20 additions and 16 deletions.
diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
@@ -69,15 +69,15 @@ jobs:
               --tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \
               --tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }}
 
-      # - name: Build Singularity
-      #   if: matrix.profile == 'singularity'
-      #   run: |
-      #     wave --conda-file "${{ matrix.files }}" \
-      #         --freeze \
-      #         --await \
-      #         --cache-repository quay.io/nf-core/wave-cache/singularity \
-      #         --tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \
-      #         --tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }} \
-      #         --singularity
+      - name: Build Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          wave --conda-file "${{ matrix.files }}" \
+              --freeze \
+              --await \
+              --cache-repository quay.io/nf-core/wave-cache/singularity \
+              --tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \
+              --tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }} \
+              --singularity
 
     # TODO Build from Dockerfiles
diff --git a/modules/nf-core/bowtie/align/environment.yml b/modules/nf-core/bowtie/align/environment.yml
@@ -1,4 +1,3 @@
-name: bowtie_samtools
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf
@@ -3,7 +3,10 @@ process BOWTIE_ALIGN {
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "community.wave.seqera.io/library/bowtie_samtools:772b3bee982574e4"
+    container ""
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'nf-core/modules/bowtie_align/singularity:bowtie_align--42e8f624908e260f' :
+        'community.wave.seqera.io/library/bowtie_samtools:772b3bee982574e4' }"
 
     input:
     tuple val(meta), path(reads)

diff --git a/modules/nf-core/bowtie/build/environment.yml b/modules/nf-core/bowtie/build/environment.yml
@@ -1,4 +1,3 @@
-name: bowtie_samtools
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/bowtie/build/main.nf b/modules/nf-core/bowtie/build/main.nf
@@ -3,7 +3,9 @@ process BOWTIE_BUILD {
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "community.wave.seqera.io/library/bowtie_samtools:772b3bee982574e4"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'nf-core/modules/bowtie_align/singularity:bowtie_align--42e8f624908e260f' :
+        'community.wave.seqera.io/library/bowtie_samtools:772b3bee982574e4' }"
 
     input:
     path fasta

diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml
@@ -1,4 +1,3 @@
-name: htslib_samtools
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf
@@ -3,7 +3,9 @@ process SAMTOOLS_VIEW {
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "community.wave.seqera.io/library/htslib_samtools:1.20--11a4e6daa46930ec"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'nf-core/modules/bowtie_align/singularity:bowtie_align--42e8f624908e260f' :
+        'community.wave.seqera.io/library/bowtie_samtools:772b3bee982574e4' }"
 
     input:
     tuple val(meta), path(input), path(index)