Fixed linting

nf-core · Oct 30, 2024 · 5f5a993 · 5f5a993
1 parent 0e7198e
commit 5f5a993
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Showing 3 changed files with 17 additions and 5 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -644,6 +644,12 @@ jobs:
             path: modules/nf-core/parabricks/fq2bammeth
           - profile: singularity
             path: modules/nf-core/parabricks/fq2bammeth
+          - profile: conda
+            path: modules/nf-core/parabricks/fq2bam
+          - profile: docker_self_hosted
+            path: modules/nf-core/parabricks/fq2bam
+          - profile: singularity
+            path: modules/nf-core/parabricks/fq2bam
           - profile: conda
             path: subworkflows/nf-core/vcf_annotate_ensemblvep
           - profile: conda

diff --git a/modules/nf-core/parabricks/fq2bam/meta.yml b/modules/nf-core/parabricks/fq2bam/meta.yml
@@ -24,11 +24,6 @@ input:
         type: file
         description: fastq.gz files
         pattern: "*.fastq.gz"
-    - interval_file:
-        type: file
-        description: (optional) file(s) containing genomic intervals for use in base
-          quality score recalibration (BQSR)
-        pattern: "*.{bed,interval_list,picard,list,intervals}"
   - - meta2:
         type: map
         description: |
@@ -45,6 +40,11 @@ input:
         type: file
         description: reference BWA index
         pattern: "*.{amb,ann,bwt,pac,sa}"
+  - - interval_file:
+        type: file
+        description: (optional) file(s) containing genomic intervals for use in base
+          quality score recalibration (BQSR)
+        pattern: "*.{bed,interval_list,picard,list,intervals}"
   - - known_sites:
         type: file
         description: (optional) known sites file(s) for calculating BQSR. markdups must

diff --git a/modules/nf-core/parabricks/fq2bam/tests/main.nf.test b/modules/nf-core/parabricks/fq2bam/tests/main.nf.test
@@ -5,6 +5,12 @@ nextflow_process {
     process "PARABRICKS_FQ2BAM"
     config "./nextflow.config"
 
+    tag "bwa/index"
+    tag "modules"
+    tag "parabricks/fq2bam"
+    tag "modules_nfcore"
+    tag "parabricks"
+
     setup {
         run("BWA_INDEX") {
             script "../../../bwa/index/main.nf"