Commit e308fa07 authored by Xavier Grand's avatar Xavier Grand
Browse files

RNAseq_XGR, modif star:main_2.7.8a.nf input index val

parent a7f5de2b
......@@ -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)
}
}
......@@ -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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