add retry

qbic-pipelines · Jan 17, 2025 · a436f43 · a436f43
1 parent 6686269
commit a436f43
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Showing 2 changed files with 4 additions and 9 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -37,6 +37,7 @@ process {
     }
 
     withName: 'BCFTOOLS_REHEADER' {
+        label        = "error_retry"
         ext.prefix   = { "${meta.label}.reheader" }
         ext.args2    = { "--output-type z --write-index=tbi" }
         publishDir = [

diff --git a/workflows/vcftomat.nf b/workflows/vcftomat.nf
@@ -126,19 +126,13 @@ workflow VCFTOMAT {
         //
         // Rename samples in vcf with the label
         //
-        ch_vcf_concat.map { meta, vcf_tbi ->
-                def sample_file = file("${workflow.workDir}/tmp/${meta.label}.txt") //${workflow.workDir}/tmp/
-                sample_file.text = "${meta.label}"
-                [ meta, vcf_tbi[0], [], sample_file ]
-            }.view()
-
         BCFTOOLS_REHEADER(
-            // Create the sample files and add them to ch_vcf_concat
+            // Create the sample files in tmp folder and add them to ch_vcf_concat
             ch_vcf_concat.map { meta, vcf_tbi ->
-                def sample_file = file("${workflow.workDir}/tmp/${meta.label}.txt") //
+                def sample_file = file("${workflow.workDir}/tmp/${meta.label}.txt")
                 sample_file.text = "${meta.label}"
                 [ meta, vcf_tbi[0], [], sample_file ]
-            },//.view(),
+            },
             [[],[]]
         )