outputs

ghga-de · Jun 24, 2024 · d456009 · d456009
1 parent 7187c57
commit d456009
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Showing 2 changed files with 3 additions and 12 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -41,7 +41,4 @@ jobs:
           if [[ $NXF_VER = '' ]]; then sleep 1200; fi
       - name: BASIC Run the basic pipeline  with docker
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
-      - name: BASIC Run the basic pipeline when --runcontig set to "ALT_HLA" (contigs does not exist in bam)
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --runcontigs "ALT_HLA"
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
diff --git a/conf/modules.config b/conf/modules.config
@@ -64,7 +64,7 @@ process {
             mode: params.publish_dir_mode
         ]
     }
-    withName: FILE_CONCATENATOR {
+    withName: SORT_NONSTANDARD_VCF {
         publishDir = [
             path: {"${params.outdir}/${meta.id}"},
             pattern: "*{.vcf.gz,vcf.gz.tbi}",
@@ -175,12 +175,6 @@ process {
             ]
         ]
     }
-        withName: 'CONVERT_TO_VCF' {
-        publishDir = [
-            path: { "${params.outdir}/test" },
-            enabled: false
-        ]
-    }  
     withName: 'BCFTOOLS_SORT' {
         publishDir = [
             path: { "${params.outdir}/${meta.id}/standard_vcf/" },
@@ -199,7 +193,7 @@ process {
 // Don't publish results for these processes
 //
 process {    
-    withName: 'GREP_SAMPLENAME|ANNOVAR|MUTATION_DISTANCE|CONTEXT_FREQUENCIES|ANNOTATE_VCF|FILTER_BY_CRIT|SNV_RELIABILITY_PIPE|DBSNP_COUNTER|FLAG_BIAS|CONFIDENCE_ANNOTATION' {
+    withName: 'GREP_SAMPLENAME|ANNOVAR|MUTATION_DISTANCE|CONTEXT_FREQUENCIES|ANNOTATE_VCF|FILTER_BY_CRIT|SNV_RELIABILITY_PIPE|DBSNP_COUNTER|FLAG_BIAS|CONFIDENCE_ANNOTATION|CONVERT_TO_VCF|FILE_CONCATENATOR' {
         publishDir = [
             path: { "${params.outdir}/test" },
             enabled: false