fix omark file renaming

Ensembl · Apr 28, 2024 · 30fac83 · 30fac83
1 parent 5204fdc
commit 30fac83
Showing 1 changed file with 7 additions and 4 deletions.
diff --git a/pipelines/nextflow/modules/omark/omark_output.nf b/pipelines/nextflow/modules/omark/omark_output.nf
@@ -21,8 +21,8 @@ include { getMetaValue } from '../utils.nf'
 process OMARK_OUTPUT {
     tag "omark_output:$gca"
     label 'default'
-    publishDir "${params.outDir}/$publish_dir/statistics", mode: 'copy'
-    //storeDir "${params.cacheDir}/$publish_dir/statistics"
+    //publishDir "${params.outDir}/$publish_dir/statistics", mode: 'copy'
+    storeDir "${params.outDir}/$publish_dir/statistics"
 
     input:
     tuple val(gca), val(dbname), val(publish_dir), path(summary_file), val(omark_dir)
@@ -31,12 +31,15 @@ process OMARK_OUTPUT {
     tuple val(gca), val(dbname), path("*.txt")
 
     script:
+    println(summary_file)
     scientific_name = getMetaValue(dbname, "species.scientific_name")[0].meta_value.toString().replaceAll("\\s", "_")
     species=scientific_name.toLowerCase()
     gca_string = gca.toLowerCase().replaceAll(/\./, "v").replaceAll(/_/, "")
-    def summary_name = summary_file
+    //def summary_name = summary_file
     summary_name = [species, gca_string, "omark", "proteins_detailed_summary.txt"].join("_")
-    summary_file.renameTo(new File(summary_file.getParent(), summary_name))
+    //summary_file= summary_name
+    omark_file = task.workDir.resolve(summary_name+'_'+summary_file)
+    //summary_file.renameTo(new File(summary_file.getParent(), summary_name))   "proteins_detailed_summary.txt"
     //"""
     //cp $summary_file $summary_name
     //"""