not publishing all files

biocorecrg · Dec 4, 2024 · 244967d · 244967d
1 parent a8f083c
commit 244967d
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Showing 2 changed files with 5 additions and 7 deletions.
diff --git a/modules/local/exorthist/merge_aligns.nf b/modules/local/exorthist/merge_aligns.nf
@@ -4,6 +4,9 @@ process MERGE_PROT_EX_INT_ALN_INFO {
 
     stageInMode 'copy'
 
+    // TODO: This needs to be changed once new publish approach
+    publishDir "${params.output}", mode: params.publish_dir_mode, pattern: "${comp_id}"
+
     input:
     tuple val(comp_id), path("FOLDERS_*"), path("*")
 
@@ -20,6 +23,7 @@ process MERGE_PROT_EX_INT_ALN_INFO {
     mv realigned_* ${comp_id}/
 
     B4_merge_PROT_EX_INT_aln_info.pl ${comp_id}
-    rmdir FOLDERS_
+    # We don't publish part files
+    mv ${comp_id}/*part_* FOLDERS_/
     """
 }
diff --git a/nextflow.config b/nextflow.config
@@ -213,12 +213,6 @@ process {
         mode: params.publish_dir_mode
       ]
   }
-  withName: 'MERGE_PROT_EX_INT_ALN_INFO' {
-    publishDir = [
-      path: { "${params.output}" },
-      mode: params.publish_dir_mode
-    ]
-  }
   withName: 'SPLIT_CLUSTERS_BY_SPECIES_PAIRS' {
     publishDir = [
       path: { "${params.output}" },