From e308fa07ba030171f13dc3245ab5a71a2a51ed7c Mon Sep 17 00:00:00 2001
From: Xavier Grand <157-xgrand@users.noreply.gitbio.ens-lyon.fr>
Date: Wed, 27 Jul 2022 09:20:15 +0200
Subject: [PATCH] RNAseq_XGR, modif star:main_2.7.8a.nf input index val
---
src/RNAseq_XGR.nf | 2 +-
src/nf_modules/star/main_2.7.8a.nf | 7 +++----
2 files changed, 4 insertions(+), 5 deletions(-)
diff --git a/src/RNAseq_XGR.nf b/src/RNAseq_XGR.nf
index 939adc6..800501f 100644
--- a/src/RNAseq_XGR.nf
+++ b/src/RNAseq_XGR.nf
@@ -153,7 +153,7 @@ workflow {
.of( idx_genome )
.set { genome_indexed_input }
genome_indexed_input.view()
- mapping_withindex(genome_indexed_input.collect(), fastp.out.fastq)
+ mapping_withindex(fastp.out.fastq)
htseq_count(mapping_withindex.out.bam, gtf_file)
}
}
diff --git a/src/nf_modules/star/main_2.7.8a.nf b/src/nf_modules/star/main_2.7.8a.nf
index e7be9f7..8e25ccd 100644
--- a/src/nf_modules/star/main_2.7.8a.nf
+++ b/src/nf_modules/star/main_2.7.8a.nf
@@ -185,7 +185,7 @@ mv ${reads_id}.Aligned.sortedByCoord.out.bam ${reads_id}.bam
"""
}
-
+params.idx = ""
process mapping_withindex {
container = "${container_url}"
label "big_mem_multi_cpus"
@@ -194,7 +194,6 @@ process mapping_withindex {
}
input:
- val(index)
tuple val(reads_id), path(reads)
output:
@@ -211,7 +210,7 @@ if (reads_id instanceof List){
if (reads.size() == 2)
"""
STAR --runThreadN ${task.cpus} \
---genomeDir ${index} \
+--genomeDir ${params.idx} \
--readFilesCommand zcat \
--readFilesIn ${reads[0]} ${reads[1]} \
--outFileNamePrefix ${reads_id}. \
@@ -224,7 +223,7 @@ mv ${reads_id}.Aligned.sortedByCoord.out.bam ${reads_id}.bam
else
"""
STAR --runThreadN ${task.cpus} \
---genomeDir ${index} \
+--genomeDir ${params.idx} \
--readFilesCommand zcat \
--readFilesIn ${reads} \
--outFileNamePrefix ${reads_id}. \
--
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