changing output dir to former system, making everything publish

modules/local/exorthist/filter_matches.nf

@@ -1,7 +1,8 @@
 process FILTER_AND_SELECT_BEST_EX_MATCHES_BY_TARGETGENE {
     tag { comp_id }
 
-    publishDir "${outdir}", mode: "copy",
+    // TODO: This needs to be changed once new publish approach
+    publishDir "${params.output}", mode: "copy",
         pattern: "best_scored_EX_matches_by_targetgene.txt",
         saveAs: { filename -> "${comp_id}/$filename" }
 
@@ -10,7 +11,6 @@ process FILTER_AND_SELECT_BEST_EX_MATCHES_BY_TARGETGENE {
     val(long_dist)
     val(medium_dist)
     val(short_dist)
-    path outdir
 
     output:
     path "*.tab", emit: filterscore_per_joining

modules/local/exorthist/merge_aligns.nf

@@ -4,14 +4,11 @@ process MERGE_PROT_EX_INT_ALN_INFO {
 
     stageInMode 'copy'
 
-    publishDir "${outdir}", mode: "copy", pattern: "${comp_id}/all_*_aln_features.txt"
-    publishDir "${outdir}", mode: "copy", pattern: "${comp_id}/EXINT_aln.gz"
-
     input:
     tuple val(comp_id), path("FOLDERS_*"), path("*")
-    path outdir
 
     output:
+    // TODO: We should only publish certain files, not all directory
     tuple val(comp_id), path("${comp_id}/"), emit: folder_jscores
     path "${comp_id}/all_*_aln_features.txt", emit: aln_features
     path "${comp_id}/EXINT_aln.gz", emit: exint_aln
@@ -23,5 +20,6 @@ process MERGE_PROT_EX_INT_ALN_INFO {
     mv realigned_* ${comp_id}/
 
     B4_merge_PROT_EX_INT_aln_info.pl ${comp_id}
+    rmdir FOLDERS_
     """
 }

modules/local/exorthist/score_matches.nf

@@ -2,11 +2,11 @@ process SCORE_EX_MATCHES {
     tag { comp_id }
     label 'big_mem'
 
-    storeDir "${outdir}/${comp_id}"
+    // TODO: This needs to be changed once new publish approach
+    storeDir "${params.output}/${comp_id}"
 
     input:
     tuple val(comp_id), path("*")
-    path outdir
 
     output:
     path "all_PROT_EX_INT_aln_features_*", emit: all_features

nextflow.config

@@ -213,6 +213,12 @@ 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}" },

subworkflows/local/exorthist/align.nf

@@ -16,7 +16,6 @@ workflow ALIGN {
     short_dist
     alignmentnum
     prevaln
-    outdir
     nofile
 
     main:
@@ -48,9 +47,7 @@ workflow ALIGN {
     realigned_exons_4_merge = REALIGN_EX_PAIRS.out.realigned_exons_4_merge
     data_4_merge = aligned_subclusters_4_splitting.groupTuple().join(realigned_exons_4_merge.groupTuple())
     // Merge alignments information
-    // TODO: Outdir approach should be eventually changed
-    outdir_ch = Channel.fromPath(outdir, checkIfExists: true).collect()
-    MERGE_PROT_EX_INT_ALN_INFO(data_4_merge, outdir_ch)
+    MERGE_PROT_EX_INT_ALN_INFO(data_4_merge)
 
     emit:
     folder_jscores = MERGE_PROT_EX_INT_ALN_INFO.out.folder_jscores

subworkflows/local/exorthist/score.nf

@@ -15,18 +15,15 @@ workflow SCORE {
     long_dist
     medium_dist
     short_dist
-    outdir
     nofile
 
     main:
-
     data_to_score = folder_jscores.join(clusters_split_ch).map{ [it[0], it[1..-1] ]}
-    // Score EX matches from aln info. TODO: This needs to be changed once new publish approach
-    outdir_ch = Channel.fromPath(outdir, checkIfExists: true).collect()
-    SCORE_EX_MATCHES(data_to_score, outdir_ch)
+    // Score EX matches from aln info.
+    SCORE_EX_MATCHES(data_to_score)
     // Filter the best matches above score cutoffs by target gene.
     all_scores_to_filt_ch = SCORE_EX_MATCHES.out.all_scores_to_filt
-    FILTER_AND_SELECT_BEST_EX_MATCHES_BY_TARGETGENE(all_scores_to_filt_ch.join(dist_ranges_ch), long_dist, medium_dist, short_dist, outdir_ch)
+    FILTER_AND_SELECT_BEST_EX_MATCHES_BY_TARGETGENE(all_scores_to_filt_ch.join(dist_ranges_ch), long_dist, medium_dist, short_dist)
     //  Join filtered scored EX matches
     filterscore_per_joining_ch = FILTER_AND_SELECT_BEST_EX_MATCHES_BY_TARGETGENE.out.filterscore_per_joining
     JOIN_FILTERED_EX_MATCHES(filterscore_per_joining_ch.collect())

workflows/main.nf

@@ -35,7 +35,6 @@ workflow MAIN {
         params.short_dist,
         params.alignmentnum,
         params.prevaln,
-        params.output,
         nofile
     )
 
@@ -47,7 +46,6 @@ workflow MAIN {
         params.long_dist,
         params.medium_dist,
         params.short_dist,
-        params.output,
         nofile
     )