Commit 4ff434d0 authored by Xavier Grand's avatar Xavier Grand
Browse files

Modif Channel idx_genome.

parent 3e2aaf8a
......@@ -145,27 +145,27 @@ workflow {
}
else {
idx_genome = "${params.idx}"
ref_1 = Channel.fromPath(params.idx +'/chrStart.txt')
ref_2 = Channel.fromPath(params.idx +'/chrNameLength.txt')
ref_3 = Channel.fromPath(params.idx +'/chrName.txt')
ref_4 = Channel.fromPath(params.idx +'/chrLength.txt')
ref_5 = Channel.fromPath(params.idx +'/exonGeTrInfo.tab')
ref_6 = Channel.fromPath(params.idx +'/exonInfo.tab')
ref_7 = Channel.fromPath(params.idx +'/geneInfo.tab')
ref_8 = Channel.fromPath(params.idx +'/Genome')
ref_9 = Channel.fromPath(params.idx +'/genomeParameters.txt')
ref_10 = Channel.fromPath(params.idx +'/SA')
ref_11 = Channel.fromPath(params.idx +'/SAindex')
ref_12 = Channel.fromPath(params.idx +'/sjdbInfo.txt')
ref_13 = Channel.fromPath(params.idx +'/transcriptInfo.tab')
ref_14 = Channel.fromPath(params.idx +'/sjdbList.fromGTF.out.tab')
ref_15 = Channel.fromPath(params.idx +'/sjdbList.out.tab')
// ref_1 = Channel.fromPath(params.idx +'/chrStart.txt')
// ref_2 = Channel.fromPath(params.idx +'/chrNameLength.txt')
// ref_3 = Channel.fromPath(params.idx +'/chrName.txt')
// ref_4 = Channel.fromPath(params.idx +'/chrLength.txt')
// ref_5 = Channel.fromPath(params.idx +'/exonGeTrInfo.tab')
// ref_6 = Channel.fromPath(params.idx +'/exonInfo.tab')
// ref_7 = Channel.fromPath(params.idx +'/geneInfo.tab')
// ref_8 = Channel.fromPath(params.idx +'/Genome')
// ref_9 = Channel.fromPath(params.idx +'/genomeParameters.txt')
// ref_10 = Channel.fromPath(params.idx +'/SA')
// ref_11 = Channel.fromPath(params.idx +'/SAindex')
// ref_12 = Channel.fromPath(params.idx +'/sjdbInfo.txt')
// ref_13 = Channel.fromPath(params.idx +'/transcriptInfo.tab')
// ref_14 = Channel.fromPath(params.idx +'/sjdbList.fromGTF.out.tab')
// ref_15 = Channel.fromPath(params.idx +'/sjdbList.out.tab')
genome_indexed_input = ref_1.concat(ref_2,ref_3,ref_4,ref_5,ref_6,ref_7,ref_8,ref_9,ref_10,ref_11,ref_12,ref_13,ref_14,ref_15)
// genome_indexed_input = ref_1.concat(ref_2,ref_3,ref_4,ref_5,ref_6,ref_7,ref_8,ref_9,ref_10,ref_11,ref_12,ref_13,ref_14,ref_15)
// Channel
// .of( idx_genome )
// .set { genome_indexed_input }
mapping_withindex(genome_indexed_input.collect(), fastp.out.fastq)
mapping_withindex(idx_genome, fastp.out.fastq)
stats_bam(mapping_withindex.out.bam)
filter_bam_mapped(mapping_withindex.out.bam)
}
......
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