From 92093a5d7513e27c5f01d34814aced39ec52e1dc Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toni.hermoso@crg.eu>
Date: Mon, 4 Nov 2024 13:48:41 +0100
Subject: [PATCH] remove params.output

---
 TODO.md                                   | 1 -
 main.nf                                   | 3 ++-
 modules/local/exorthist/filter_matches.nf | 3 ++-
 modules/local/exorthist/merge_aligns.nf   | 5 +++--
 modules/local/exorthist/plot/get_exons.nf | 3 ++-
 subworkflows/local/exorthist/align.nf     | 3 ++-
 subworkflows/local/exorthist/score.nf     | 2 +-
 workflows/main.nf                         | 1 +
 workflows/plot.nf                         | 1 +
 9 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/TODO.md b/TODO.md
index b20a173..edbb4ad 100644
--- a/TODO.md
+++ b/TODO.md
@@ -1,3 +1,2 @@
-- Review params.output from modules (optional)
 - Add stub to modules (optional)
 - Include colors into the terminal messages (optional)
diff --git a/main.nf b/main.nf
index 0b87e61..5cc6409 100644
--- a/main.nf
+++ b/main.nf
@@ -47,7 +47,8 @@ workflow {
             params.relevant_exs,
             params.ordered_species,
             params.isoformID,
-            params.sub_orthologs
+            params.sub_orthologs,
+            params.output
         )
 
     } else {
diff --git a/modules/local/exorthist/filter_matches.nf b/modules/local/exorthist/filter_matches.nf
index 00dfc1e..1c9f883 100644
--- a/modules/local/exorthist/filter_matches.nf
+++ b/modules/local/exorthist/filter_matches.nf
@@ -1,7 +1,7 @@
 process FILTER_AND_SELECT_BEST_EX_MATCHES_BY_TARGETGENE {
     tag { comp_id }
 
-    publishDir "${params.output}", mode: "copy",
+    publishDir "${outdir}", mode: "copy",
         pattern: "best_scored_EX_matches_by_targetgene.txt",
         saveAs: { filename -> "${comp_id}/$filename" }
 
@@ -10,6 +10,7 @@ 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
diff --git a/modules/local/exorthist/merge_aligns.nf b/modules/local/exorthist/merge_aligns.nf
index 95defa6..1894a4a 100644
--- a/modules/local/exorthist/merge_aligns.nf
+++ b/modules/local/exorthist/merge_aligns.nf
@@ -4,11 +4,12 @@ process MERGE_PROT_EX_INT_ALN_INFO {
 
     stageInMode 'copy'
 
-    publishDir "${params.output}", mode: "copy", pattern: "${comp_id}/all_*_aln_features.txt"
-    publishDir "${params.output}", mode: "copy", pattern: "${comp_id}/EXINT_aln.gz"
+    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:
     tuple val(comp_id), path("${comp_id}/"), emit: folder_jscores
diff --git a/modules/local/exorthist/plot/get_exons.nf b/modules/local/exorthist/plot/get_exons.nf
index d026b20..aa2607d 100644
--- a/modules/local/exorthist/plot/get_exons.nf
+++ b/modules/local/exorthist/plot/get_exons.nf
@@ -1,12 +1,13 @@
 process GET_ISOFORM_EXONS {
     tag "${isoformID}"
     label 'pandas'
-    publishDir "${params.output}/${geneID}/processed_table", mode: 'copy'
+    publishDir "${outdir}/${geneID}/processed_table", mode: 'copy'
 
     input:
     val(isoformID)
     tuple val(species), path(exons_info), path(overlap_info)
     val(geneID)
+    path outdir
 
     output:
     stdout emit: isoform_interesting_exs
diff --git a/subworkflows/local/exorthist/align.nf b/subworkflows/local/exorthist/align.nf
index f0e5fbc..fd544d7 100644
--- a/subworkflows/local/exorthist/align.nf
+++ b/subworkflows/local/exorthist/align.nf
@@ -16,6 +16,7 @@ workflow ALIGN {
     short_dist
     alignmentnum
     prevaln
+    outdir
 
     main:
 
@@ -46,7 +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
-    MERGE_PROT_EX_INT_ALN_INFO(data_4_merge)
+    MERGE_PROT_EX_INT_ALN_INFO(data_4_merge, outdir)
 
     emit:
     folder_jscores = MERGE_PROT_EX_INT_ALN_INFO.out.folder_jscores
diff --git a/subworkflows/local/exorthist/score.nf b/subworkflows/local/exorthist/score.nf
index 54fcd65..df838ee 100644
--- a/subworkflows/local/exorthist/score.nf
+++ b/subworkflows/local/exorthist/score.nf
@@ -24,7 +24,7 @@ workflow SCORE {
     SCORE_EX_MATCHES(data_to_score, outdir)
     // 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)
+    FILTER_AND_SELECT_BEST_EX_MATCHES_BY_TARGETGENE(all_scores_to_filt_ch.join(dist_ranges_ch), long_dist, medium_dist, short_dist, outdir)
     //  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())
diff --git a/workflows/main.nf b/workflows/main.nf
index abd68f8..8f3cfd7 100644
--- a/workflows/main.nf
+++ b/workflows/main.nf
@@ -31,6 +31,7 @@ workflow MAIN {
         params.short_dist,
         params.alignmentnum,
         params.prevaln
+        params.output
     )
 
     SCORE(
diff --git a/workflows/plot.nf b/workflows/plot.nf
index acd18fe..e663819 100644
--- a/workflows/plot.nf
+++ b/workflows/plot.nf
@@ -17,6 +17,7 @@ workflow PLOT {
     ordered_species
     isoformID
     sub_orthologs
+    outdir
 
     main: