From 0e61e65b49bf30e47b102d150b2759b5771b20fa Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toni.hermoso@crg.eu>
Date: Fri, 25 Oct 2024 12:34:50 +0200
Subject: [PATCH] fixing all null stuff

---
 modules/local/exorthist/collapse_matches.nf | 2 +-
 modules/local/exorthist/recluster_exs.nf    | 2 +-
 modules/local/exorthist/recluster_genes.nf  | 2 +-
 subworkflows/local/exorthist/cluster.nf     | 2 +-
 subworkflows/local/exorthist/score.nf       | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/local/exorthist/collapse_matches.nf b/modules/local/exorthist/collapse_matches.nf
index 74ef11b..7593492 100644
--- a/modules/local/exorthist/collapse_matches.nf
+++ b/modules/local/exorthist/collapse_matches.nf
@@ -10,7 +10,7 @@ process COLLAPSE_OVERLAPPING_MATCHES {
     path "overlapping_EXs_by_species.tab", emit: overlapping_exs
 
     script:
-    def bonafide = bonafide_pairs.name != 'NO_FILE' ? "-b ${bonafide_pairs}" : ''
+    def bonafide = bonafide_pairs.name != 'null' ? "-b ${bonafide_pairs}" : ''
     """
     C3_count_matches_by_EX.pl ${scores} EX_matches_count_by_species.tab ${bonafide}
     C4_get_overlapping_EXs.pl -i EX_matches_count_by_species.tab -o overlapping_EXs_by_species.tab
diff --git a/modules/local/exorthist/recluster_exs.nf b/modules/local/exorthist/recluster_exs.nf
index ae42fc0..d9c9bc1 100644
--- a/modules/local/exorthist/recluster_exs.nf
+++ b/modules/local/exorthist/recluster_exs.nf
@@ -13,7 +13,7 @@ process RECLUSTER_EXS_BY_SPECIES_PAIR {
     path "reclustered_EXs_*.tab", emit: recl_exs
 
     when:
-    orthopairs.name != 'NO_FILE'
+    orthopairs.name != 'null'
 
     script:
     def combid1 = combid.replace("-", "_")
diff --git a/modules/local/exorthist/recluster_genes.nf b/modules/local/exorthist/recluster_genes.nf
index 2f9a8c8..171b067 100644
--- a/modules/local/exorthist/recluster_genes.nf
+++ b/modules/local/exorthist/recluster_genes.nf
@@ -12,7 +12,7 @@ process RECLUSTER_GENES_BY_SPECIES_PAIR {
     tuple val(combid), path("reclustered_genes_*.tab"), emit: recl_genes_for_rec_exons
 
     when:
-    orthopairs.name != 'NO_FILE'
+    orthopairs.name != 'null'
 
     script:
     def (species1, species2) = combid.split("-")
diff --git a/subworkflows/local/exorthist/cluster.nf b/subworkflows/local/exorthist/cluster.nf
index 70da0c0..6986bed 100644
--- a/subworkflows/local/exorthist/cluster.nf
+++ b/subworkflows/local/exorthist/cluster.nf
@@ -21,7 +21,7 @@ workflow CLUSTER {
     if (orthopairs) {
         orthopairs_ch = Channel.fromPath(orthopairs, checkIfExists: true).collect()
     } else {
-        orthopairs_ch = Channel.fromPath("/path/to/NO_FILE").collect()
+        orthopairs_ch = Channel.fromPath("/dev/null").collect()
     }
 
     FORMAT_EX_CLUSTERS_INPUT(score_exon_hits_pairs, clusterfile_ch, orthogroupnum)
diff --git a/subworkflows/local/exorthist/score.nf b/subworkflows/local/exorthist/score.nf
index df15f9b..ac07990 100644
--- a/subworkflows/local/exorthist/score.nf
+++ b/subworkflows/local/exorthist/score.nf
@@ -34,7 +34,7 @@ workflow SCORE {
     if ( bonafide_pairs ) {
         COLLAPSE_OVERLAPPING_MATCHES(filtered_all_scores, bonafide_pairs)
     } else {
-        COLLAPSE_OVERLAPPING_MATCHES(filtered_all_scores, Channel.fromPath("/path/to/NO_FILE").collect())
+        COLLAPSE_OVERLAPPING_MATCHES(filtered_all_scores, Channel.fromPath("/dev/null").collect())
     }
 
     emit: