From 4ff434d0ca4e1e0602485bf4c12d9992920c1187 Mon Sep 17 00:00:00 2001
From: Xavier Grand <xavier.grand@ens-lyon.fr>
Date: Fri, 5 Aug 2022 10:58:58 +0200
Subject: [PATCH] Modif Channel idx_genome.
---
src/RNAseq_XGR.nf | 34 +++++++++++++++++-----------------
1 file changed, 17 insertions(+), 17 deletions(-)
diff --git a/src/RNAseq_XGR.nf b/src/RNAseq_XGR.nf
index 33ec322..63cb663 100644
--- a/src/RNAseq_XGR.nf
+++ b/src/RNAseq_XGR.nf
@@ -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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