Merge pull request #1 from MarieLataretu/feature/better-publishing

tweak publishing of results
MarieLataretu · Nov 11, 2023 · 9012b8d · 9012b8d
2 parents c13fb30 + 9aa7442
commit 9012b8d
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diff --git a/modules/bwa/index/main.nf b/modules/bwa/index/main.nf
@@ -2,9 +2,6 @@ process BWA_INDEX {
     // custom label for easier identification in the log file
     tag "$reference.simpleName"
 
-    // copy the results to a defined folder
-    publishDir "${params.outdir}", mode: 'copy'
-
     // engine settings
     conda 'bioconda::bwa=0.7.17 bioconda::samtools=1.18'
     container 'rkimf1/bwa-samtools:0.7.17--6eae1f3'

diff --git a/modules/bwa/mem/main.nf b/modules/bwa/mem/main.nf
@@ -2,8 +2,8 @@ process BWA_MEM {
     // custom label for easier identification in the log file
     tag "$name"
 
-    // copy the results to a defined folder
-    publishDir "${params.outdir}", mode: 'copy'
+    // copy the BAM file to a defined folder
+    publishDir "${params.outdir}", mode: 'copy', pattern: "*.bam"
 
     // engine settings
     conda 'bioconda::bwa=0.7.17 bioconda::samtools=1.18'