fixing all null stuff

biocorecrg · Oct 25, 2024 · 0e61e65 · 0e61e65
1 parent 928eb47
commit 0e61e65
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Showing 5 changed files with 5 additions and 5 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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: