From 6f67c65ca46aaacc61450e79ee2475d81363dd38 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 2 Jun 2021 10:49:47 +0200
Subject: [PATCH] bwa: add mapping workflow
---
src/nf_modules/bwa/main.nf | 13 +++++++++++++
1 file changed, 13 insertions(+)
diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf
index 1e4da4bd..a70f4bb3 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -2,6 +2,19 @@ version = "0.7.17"
container_url = "lbmc/bwa:${version}"
+workflow mapping {
+ take:
+ fasta
+ fastq
+ main:
+ index_fasta(fasta)
+ mapping_fastq(index_fasta.out.index.collect(), fastq)
+ emit:
+ bam: mapping_fastq.out.bam
+ report: mapping_fastq.out.report
+}
+
+
params.index_fasta = ""
params.index_fasta_out = ""
process index_fasta {
--
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