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Feature/count reads #91

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9cc4737
- add count_reads module
mauro-saporita Aug 24, 2023
fd1e528
add count reads for single end files
mauro-saporita Aug 28, 2023
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19 changes: 16 additions & 3 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -57,10 +57,23 @@ process {
]
}

withName: COUNT_READS {
publishDir = [
[
path: { "${params.outdir}/count_reads/${meta.id}" },
mode: params.publish_dir_mode,
]
]
}




withName: COUNT_READS_AFTER_TRIMMING {
publishDir = [
[
path: { "${params.outdir}/count_reads_after_trimming/${meta.id}" },
mode: params.publish_dir_mode,
]
]
}

withName: FASTQC {
ext.args = '--quiet'
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39 changes: 39 additions & 0 deletions modules/local/count_reads.nf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,39 @@
process COUNT_READS {
tag "$meta.id"
label 'process_medium'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'nfcore/dualrnaseq:dev' :
'nfcore/dualrnaseq:dev' }"

input:
tuple val(meta), path(reads)

output:
tuple val(meta), path('*.txt'), emit: read_counts

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

if (reads instanceof Path || reads.size() == 1) {
// Code to process a single file
"""
count_1=\$((\$(zcat ${reads[0]} | wc -l) / 4))
echo "${reads[0].baseName}\t\$count_1" > ${reads[0].baseName}_counts.txt
"""
} else if (reads instanceof Path || reads.size() == 2) {
// Code to process two files
"""
count_1=\$((\$(zcat ${reads[0]} | wc -l) / 4))
count_2=\$((\$(zcat ${reads[1]} | wc -l) / 4))
echo "${reads[0].baseName}\t\$count_1" > ${reads[0].baseName}_counts.txt
echo "${reads[1].baseName}\t\$count_2" > ${reads[1].baseName}_counts.txt
"""
} else {
"""
echo "Error: Input 'reads' should contain either one or two files."
exit 1
"""
}
}
6 changes: 3 additions & 3 deletions modules/nf-core/fastqc/main.nf
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21 changes: 15 additions & 6 deletions workflows/dualrnaseq.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -72,11 +72,13 @@ include { SALMON_ALIGNMENT_BASED } from '../subworkflows/local/salmon_alignment_
//
// MODULE: Installed directly from nf-core/modules
//
include { FASTQC } from '../modules/nf-core/fastqc/main'
include { FASTQC as FASTQC_AFTER_TRIMMING } from '../modules/nf-core/fastqc/main'
include { CUTADAPT } from '../modules/nf-core/cutadapt/main'
include { MULTIQC } from '../modules/nf-core/multiqc/main'
include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
include { COUNT_READS } from '../modules/local/count_reads'
include { COUNT_READS as COUNT_READS_AFTER_TRIMMING } from '../modules/local/count_reads'
include { FASTQC } from '../modules/nf-core/fastqc/main'
include { FASTQC as FASTQC_AFTER_TRIMMING } from '../modules/nf-core/fastqc/main'
include { CUTADAPT } from '../modules/nf-core/cutadapt/main'
include { MULTIQC } from '../modules/nf-core/multiqc/main'
include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand All @@ -99,12 +101,17 @@ workflow DUALRNASEQ {
)
ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)

COUNT_READS (
INPUT_CHECK.out.reads
)

ch_count_reads_merged = Channel.fromPath( "${params.outdir}/count_reads/*" ).collectFile(name: 'count_reads_merged.txt').view()

if (!(params.skip_tools && params.skip_tools.split(',').contains('fastqc'))) {
FASTQC(INPUT_CHECK.out.reads)
ch_versions = ch_versions.mix(FASTQC.out.versions.first())
}

ch_reads = INPUT_CHECK.out.reads
if (!(params.skip_tools && params.skip_tools.split(',').contains('cutadapt'))) {
CUTADAPT(INPUT_CHECK.out.reads)
ch_reads = CUTADAPT.out.reads
Expand All @@ -114,6 +121,8 @@ workflow DUALRNASEQ {
if (!(params.skip_tools && (params.skip_tools.split(',').contains('fastqc') || params.skip_tools.split(',').contains('cutadapt')))) {
FASTQC_AFTER_TRIMMING(ch_reads)
ch_versions = ch_versions.mix(FASTQC_AFTER_TRIMMING.out.versions.first())
COUNT_READS_AFTER_TRIMMING (INPUT_CHECK.out.reads)
ch_count_reads_merged = Channel.fromPath( "${params.outdir}/count_reads/*" ).collectFile(name: 'count_reads_after_trimming_merged.txt').view()
}


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