Fix ciriquant keyerror

Author: nictru

conf/modules.config

@@ -875,7 +875,7 @@ process {
             [
                 "-v FS='\\t'",
                 "-v OFS='\\t'",
-                "'{ \$4 = \"circ_\" \$1 \":\" \$2 \"-\" \$3",
+                "'{ \$4 = \$1 \":\" \$2 \"-\" \$3",
                 (params.consider_strand ? " \":\" \$6" : ""),
                 "; print }'",
             ].join(' ').trim()
@@ -983,7 +983,7 @@ process {
     }
 
     withName: MARK_CIRCULAR {
-        ext.args   = "'{ if (/^>.+:[0-9]+-[0-9]+/) { print \$1 \"\\tC\" } else { print } }'"
+        ext.args   = "'{ if (/^>.+:[0-9]+-[0-9]+(:[+-])?/) { print \$1 \"\\tC\" } else { print } }'"
         ext.suffix = "marked.fasta"
         publishDir = [
             path: { "${params.outdir}/5_quantification/psirc/transcriptome" },

modules/local/quantification/split_types/main.nf

@@ -13,7 +13,7 @@ process SPLIT_TYPES {
     output:
     tuple val(meta), path("linear.tsv")  , emit: linear
     tuple val(meta), path("circular.tsv"), emit: circular
-    path "versions.yml"                   , emit: versions
+    path "versions.yml"                  , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,7 +22,7 @@ process SPLIT_TYPES {
     """
     awk -F'\\t' \\
         'NR==1 {print > "circular.tsv"; print > "linear.tsv"} \\
-        NR>1 {if (\$1 ~ /^circ_/) print > "circular.tsv"; else print > "linear.tsv"}' ${input}
+        NR>1 {if (\$1 ~ /^.+:[0-9]+-[0-9]+(:[+-])?/) print > "circular.tsv"; else print > "linear.tsv"}' ${input}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":