From b412a7fab77a428fbeee9af0c94eca763f9ad581 Mon Sep 17 00:00:00 2001
From: xgrand <xavier.grand@ens-lyon.fr>
Date: Fri, 6 Aug 2021 10:10:18 +0200
Subject: [PATCH] indexed genome params
---
src/chipster.nf | 24 +++++++++++++++---------
1 file changed, 15 insertions(+), 9 deletions(-)
diff --git a/src/chipster.nf b/src/chipster.nf
index 2546e99a..5855b0a5 100644
--- a/src/chipster.nf
+++ b/src/chipster.nf
@@ -32,9 +32,8 @@ params.genome = "data/tinyTestDataset/*.fasta"
@type: File
*/
-/*
-params.folder = "project"
-/* project output folder
+params.idxgenome = ""
+/* already indexed reference genome
@Type: String
*/
@@ -46,7 +45,8 @@ params.folder = "project"
*/
log.info "fastq files : ${params.fastq}"
-log.info "genome files : ${params.genome}"
+log.info "genome file : ${params.genome}"
+log.info "indexed genome file : ${params.idxgenome}"
/*
log.info "paired-end data: ${params.paired_end}"
@@ -74,6 +74,10 @@ Channel
.fromFilePairs( params.genome, size: -1 )
.set { genome_file }
+Channel
+ .fromPath( params.idxgenome )
+ .set { genome_idx }
+
/*
****************************************************************
Imports
@@ -113,11 +117,13 @@ workflow {
fastqc_preprocessed.out.report
).collect()
)
- // index reference genome
- index_fasta(genome_file)
-
- // mapping preprocessed reads
- mapping_fastq(index_fasta.out.index.collect(), fastp_default.out.fastq)
+ // index reference genome & mapping preprocessed reads
+ if (!params.idxgenome) {
+ index_fasta(genome_file)
+ mapping_fastq(index_fasta.out.index.collect(), fastp_default.out.fastq)
+ } else {
+ mapping_fastq(genome_idx.collect(), fastp_default.out.fastq)
+ }
// filter bam - remove reads with quality <30
filter_bam_quality(mapping_fastq.out.bam)
--
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