Newer
Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
params.fastq = "$baseDir/data/fastq/*.fastq"
params.index = "$baseDir/data/index/*.index*"
params.mean = 300
params.sd = 100
log.info "fastq files : ${params.fastq}"
log.info "index files : ${params.index}"
log.info "mean read size: ${params.mean}"
log.info "sd read size: ${params.sd}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
Channel
.fromPath( params.index )
.ifEmpty { error "Cannot find any index files matching: ${params.index}" }
.set { index_files }
process mapping_fastq {
tag "$reads.baseName"
cpus 4
publishDir "results/mapping/quantification/", mode: 'copy'
input:
file reads from fastq_files
file index from index_files.toList()
output:
file "*" into count_files
script:
index_name = (index[0].baseName =~ /(.*)\.\d/)[0][1]
"""
rsem-calculate-expression --bowtie2 \
--bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
--bowtie2-sensitivity-level "very_sensitive" \
--fragment-length-mean ${params.mean} --fragment-length-sd ${params.sd} \
--output-genome-bam -p ${task.cpus} \
${reads} ${index_name} ${reads.baseName} \
> ${reads.baseName}_rsem_bowtie2_report.txt
"""
}