Merge branch 'master' into regtools_bump_versions

nf-core · Nov 22, 2024 · 4920542 · 4920542
2 parents b4eeae5 + d5d0870
commit 4920542
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Showing 5 changed files with 6 additions and 9 deletions.
diff --git a/.github/workflows/gpu-tests.yml b/.github/workflows/gpu-tests.yml
@@ -60,7 +60,7 @@ jobs:
 
       - name: List nf-test files
         id: list
-        uses: adamrtalbot/detect-nf-test-changes@e114e734c3bfa4599151087dcbc457ff38e5bf2c
+        uses: adamrtalbot/detect-nf-test-changes@6bf6fd9fe0fb63a0362fb0e09de5acb6d055a754 # v0.0.5
         with:
           head: ${{ github.sha }}
           base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha }}

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -82,7 +82,7 @@ jobs:
               .map(path => path.replace('modules/nf-core/', '')
               .split('/')
               .slice(0, 2)
-              .filter(x => x !== 'main.nf' && x !== 'tests')
+              .filter(x => x !== 'main.nf' && x !== 'tests' && x !== 'meta.yml' && x !== 'environment.yml')
               .join('/')))];
 
       - name: Get subworkflow name
@@ -94,7 +94,7 @@ jobs:
               .map(path => path.replace('subworkflows/nf-core/', '')
               .split('/')
               .slice(0,2)
-              .filter(x => x !== 'main.nf' && x !== 'tests')
+              .filter(x => x !== 'main.nf' && x !== 'tests' && x !== 'meta.yml' && x !== 'environment.yml')
               .join('/')))];
 
       - name: debug

diff --git a/modules/nf-core/nonpareil/curve/main.nf b/modules/nf-core/nonpareil/curve/main.nf
@@ -11,7 +11,7 @@ process NONPAREIL_CURVE {
     tuple val(meta), path(npo)
 
     output:
-    tuple val(meta), path("*.png"), emit: png
+    tuple val(meta), path("*.png"), optional: true, emit: png
     path "versions.yml"           , emit: versions
 
     when:

diff --git a/modules/nf-core/pilon/main.nf b/modules/nf-core/pilon/main.nf
@@ -40,7 +40,7 @@ process PILON {
     PILON_JAR=\$(dirname \$(which pilon))/../share/pilon*/pilon.jar
     java -Xmx${mem_mb}M -jar \$PILON_JAR \\
         --genome $fasta \\
-        --output ${meta.id} \\
+        --output ${prefix} \\
         $args \\
         --$pilon_mode $bam
 

diff --git a/modules/nf-core/quartonotebook/main.nf b/modules/nf-core/quartonotebook/main.nf
@@ -1,7 +1,4 @@
-include {
-    dumpParamsYaml ;
-    indentCodeBlock
-} from "./parametrize"
+include { dumpParamsYaml ; indentCodeBlock } from "./parametrize"
 
 // NB: You'll likely want to override this with a container containing all
 // required dependencies for your analyses. Or use wave to build the container