From c4792fa5e80914402076e0a2e8b5fc8727f31a6c Mon Sep 17 00:00:00 2001
From: xgrand <xavier.grand@ens-lyon.fr>
Date: Fri, 6 Aug 2021 10:56:57 +0200
Subject: [PATCH] idx genome mod
---
src/chipster.nf | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/src/chipster.nf b/src/chipster.nf
index 5855b0a5..8cadbd76 100644
--- a/src/chipster.nf
+++ b/src/chipster.nf
@@ -32,7 +32,7 @@ params.genome = "data/tinyTestDataset/*.fasta"
@type: File
*/
-params.idxgenome = ""
+params.idxgenome = "data/tinyTestDataset/*.fasta.fai*"
/* already indexed reference genome
@Type: String
@@ -117,13 +117,17 @@ workflow {
fastqc_preprocessed.out.report
).collect()
)
+
+ mapping_fastq(genome_idx.collect(), fastp_default.out.fastq)
+
// index reference genome & mapping preprocessed reads
- if (!params.idxgenome) {
+ /*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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