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Commit 97103dc2 authored by alapendr's avatar alapendr
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Rnaseq.nf : update

parent d3a661db
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...@@ -128,7 +128,7 @@ process index_fasta { ...@@ -128,7 +128,7 @@ process index_fasta {
publishDir "results/mapping/index/", mode: 'copy' publishDir "results/mapping/index/", mode: 'copy'
input: input:
file fasta from fasta_files file fasta from fasta_files_extracted
output: output:
file "*.index*" into index_files file "*.index*" into index_files
...@@ -152,8 +152,8 @@ process mapping_fastq { ...@@ -152,8 +152,8 @@ process mapping_fastq {
publishDir "results/mapping/quantification/", mode: 'copy' publishDir "results/mapping/quantification/", mode: 'copy'
input: input:
file reads from fastq_files file reads from fastq_files_trim
file index from index_files.toList() file index from index_files
output: output:
file "*" into counts_files file "*" into counts_files
...@@ -168,31 +168,5 @@ ${reads[0]} ${reads[1]} &> ${reads[0].baseName}_kallisto_report.txt ...@@ -168,31 +168,5 @@ ${reads[0]} ${reads[1]} &> ${reads[0].baseName}_kallisto_report.txt
} }
/*
* for single-end data
*/
process mapping_fastq {
tag "$reads.baseName"
cpus 4
publishDir "results/mapping/quantification/", mode: 'copy'
input:
file reads from fastq_files_trim
file index from index_files
output:
file "*" into count_files
script:
"""
mkdir ${reads.baseName}
kallisto quant -i ${index} -t ${task.cpus} --single
--bias --bootstrap-samples 100 -o ${reads.baseName} \
-l ${params.mean} -s ${params.sd} -o ./ \
${reads} > ${reads.baseName}_kallisto_report.txt
"""
}
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