From 181102e8bc493f923fa79e7e0f1f6ed1e99d207b Mon Sep 17 00:00:00 2001
From: Xavier Grand <157-xgrand@users.noreply.gitbio.ens-lyon.fr>
Date: Mon, 25 Jul 2022 13:28:27 +0200
Subject: [PATCH] add STAR and HTseq to RNAseq_XGR.nf
---
src/RNAseq_XGR.nf | 3 ++-
src/nf_modules/star/main_2.7.8a.nf | 3 +++
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/src/RNAseq_XGR.nf b/src/RNAseq_XGR.nf
index cc2ecc8..f456e70 100644
--- a/src/RNAseq_XGR.nf
+++ b/src/RNAseq_XGR.nf
@@ -65,7 +65,8 @@ params.fasta = ""
params.idx = ""
params.fastp_out = "$params.project/fastp/"
-// params.star_mapping_fastq_out = "$params.project/STAR/"
+params.star_mapping_fastq_out = "$params.project/STAR/"
+params.star_index_out = "$params.project/STARindex/"
/*
****************************************************************
diff --git a/src/nf_modules/star/main_2.7.8a.nf b/src/nf_modules/star/main_2.7.8a.nf
index a711426..44e6693 100644
--- a/src/nf_modules/star/main_2.7.8a.nf
+++ b/src/nf_modules/star/main_2.7.8a.nf
@@ -22,6 +22,9 @@ gffread ${gff3_file} -T -o ${genome_id}.gtf
process index_with_gtf {
container = "${container_url}"
label "big_mem_multi_cpus"
+ if (params.star_index_out != "") {
+ publishDir "results/${params.star_index_out}", mode: 'copy'
+ }
input:
tuple val(genome_id), path(genome_fasta)
--
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