Fix bug in salmon/index module when generating decoys (#3043)

* Fix bug in salmon/index module when generating decoys * Fix spacing
nf-core · Mar 16, 2023 · cfef219 · cfef219
1 parent 0263ccf
commit cfef219
Showing 1 changed file with 5 additions and 4 deletions.
diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf
@@ -12,18 +12,18 @@ process SALMON_INDEX {
     path transcript_fasta
 
     output:
-    path "salmon"       , emit: index
-    path "versions.yml" , emit: versions
+    path "salmon"      , emit: index
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def get_decoy_ids = "grep '^>' $genome_fasta | cut -d ' ' -f 1 > decoys.txt"
+    def get_decoy_ids = "grep '^>' $genome_fasta | cut -d ' ' -f 1 | cut -d \$'\\t' -f 1 > decoys.txt"
     def gentrome      = "gentrome.fa"
     if (genome_fasta.endsWith('.gz')) {
-        get_decoy_ids = "grep '^>' <(gunzip -c $genome_fasta) | cut -d ' ' -f 1 > decoys.txt"
+        get_decoy_ids = "grep '^>' <(gunzip -c $genome_fasta) | cut -d ' ' -f 1 | cut -d \$'\\t' -f 1 > decoys.txt"
         gentrome      = "gentrome.fa.gz"
     }
     """
@@ -38,6 +38,7 @@ process SALMON_INDEX {
         -d decoys.txt \\
         $args \\
         -i salmon
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g")