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lines changed Original file line number Diff line number Diff line change @@ -71,18 +71,21 @@ workflow PREPARE_GENOME {
7171 }
7272 }
7373 else if (gff) {
74- if (gff. endsWith(' .gz' )) {
74+ if (gff. endsWith(' .gz' )) {
7575 ch_gff = GUNZIP_GFF ([[:], file(gff, checkIfExists : true )]). gunzip. map { it[1 ] }
7676 ch_versions = ch_versions. mix(GUNZIP_GFF . out. versions)
7777 }
7878 else {
7979 ch_gff = Channel . value(file(gff, checkIfExists : true ))
8080 }
8181
82+ //
83+ // Detect gff file name stripped of extension and .gz
84+ //
8285 extension = (gff - ' .gz' ). tokenize(' .' )[-1 ]
8386 id = gff. toString() - ' .gz' - " .${ extension} "
8487
85- ch_gtf = GFFREAD (ch_gff. map{ [[id :id], it]}, []). gtf. map { it[1 ] }
88+ ch_gtf = GFFREAD (ch_gff. map { [[id : id], it] }, []). gtf. map { it[1 ] }
8689
8790 ch_versions = ch_versions. mix(GFFREAD . out. versions)
8891 }
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