polish

TheJacksonLaboratory · Aug 16, 2024 · 477709b · 477709b
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commit 477709b
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Showing 2 changed files with 5 additions and 6 deletions.
diff --git a/modules/bcftools/bcftools_gtct2vcf.nf b/modules/bcftools/bcftools_gtct2vcf.nf
@@ -8,15 +8,14 @@ process BCFTOOLS_GTC2VCF {
     errorStrategy {(task.exitStatus == 140) ? {log.info "\n\nError code: ${task.exitStatus} for task: ${task.name}. Likely caused by the task wall clock: ${task.time} or memory: ${task.memory} being exceeded.\nAttempting orderly shutdown.\nSee .command.log in: ${task.workDir} for more info.\n\n"; return 'finish'}.call() : 'finish'}
 
     container 'quay.io/jaxcompsci/gtc2vcf_with_tools:v2'
-    publishDir "${params.pubdir}/${ params.organize_by=='sample' ? sampleID : 'bcftools' }", mode: 'copy'
+    publishDir "${params.pubdir}/${ params.organize_by=='sample' ? sampleID : 'bcftools' }", pattern: "*.{vcf,tsv}", mode: 'copy'
 
     input:
     tuple val(sampleID), val(meta), path(gtc)
 
     output:
-    tuple val(sampleID), val(meta), path('*_convert.bcf'), path('*_convert.bcf.csi'), path('*_convert.vcf'), path('*_convert.tsv'), emit: gtc2vcf
+    tuple val(sampleID), val(meta), path('*_convert.bcf'), path('*_convert.bcf.csi'), path('*_convert.vcf'), path('*_convert_info.tsv'), emit: gtc2vcf
 
-
     script:
     """
     bcftools +gtc2vcf --no-version -Ou \
@@ -25,7 +24,7 @@ process BCFTOOLS_GTC2VCF {
     --egt ${params.egt_file} \
     --gtcs ./ \
     --fasta-ref ${params.ref_fa} \
-    --extra ${sampleID}_convert.tsv | \
+    --extra ${sampleID}_convert_info.tsv | \
     bcftools sort -Ou -T ./bcftools. | \
     bcftools norm --no-version -Ob -c x -f ${params.ref_fa} | \
     tee ${sampleID}_convert.bcf | \

diff --git a/modules/illumina/iaap_cli.nf b/modules/illumina/iaap_cli.nf
@@ -10,8 +10,8 @@ process IAAP_CLI {
 
   container 'quay.io/jaxcompsci/gtc2vcf_with_tools:v2'
 
-  publishDir "${params.pubdir}/${ params.organize_by=='sample' ? sampleID : 'iaap_cli' }", pattern: "*.gtc", mode:'copy'
-  publishDir "${params.pubdir}/${ params.organize_by=='sample' ? sampleID : 'iaap_cli' }", pattern: "*.log", mode:'copy'
+  publishDir "${params.pubdir}/${ params.organize_by=='sample' ? sampleID : 'iaap_cli' }", pattern: "*.gtc", mode:'copy', enabled: params.keep_intermediate
+  publishDir "${params.pubdir}/${ params.organize_by=='sample' ? sampleID : 'iaap_cli' }", pattern: "*.log", mode:'copy', enabled: params.keep_intermediate
 
   input:
   tuple val(sampleID), val(meta), path(red_idat), path(green_idat)