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RNAseq.nf
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RNAseq.nf
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#!/usr/bin/env nextflow
// Copyright (C) 2017 IARC/WHO
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
// You should have received a copy of the GNU General Public License
// along with this program. If not, see <http://www.gnu.org/licenses/>.
params.input_folder = null
params.input_file = null
params.ref_folder = null
params.gtf = null
params.bed = null
params.cpu = 4
params.cpu_gatk = 1
params.mem = 50
params.mem_QC = 2
params.fastq_ext = "fq.gz"
params.suffix1 = "_1"
params.suffix2 = "_2"
params.output_folder= "."
params.ref = "ref.fa"
params.snp_vcf = "dbsnp.vcf"
params.indel_vcf = "Mills_1000G_indels.vcf"
params.RG = "PL:ILLUMINA"
params.STAR_mapqUnique = 255
params.stranded = "no"
params.hisat2_idx = "genome_tran"
params.cpu_trim = 15
params.htseq_maxreads = null //default value of htseq-count is 30000000
params.multiqc_config = 'NO_FILE'
params.sjtrim = null
params.recalibration= null
params.cutadapt = null
params.hisat2 = null
params.help = null
log.info ""
log.info "--------------------------------------------------------"
log.info " RNAseq-nf 2.4.0: alignment, QC, and reads counting workflow for RNA sequencing "
log.info "--------------------------------------------------------"
log.info "Copyright (C) IARC/WHO"
log.info "This program comes with ABSOLUTELY NO WARRANTY; for details see LICENSE"
log.info "This is free software, and you are welcome to redistribute it"
log.info "under certain conditions; see LICENSE for details."
log.info "--------------------------------------------------------"
log.info ""
if (params.help) {
log.info '-------------------------------------------------------------'
log.info ' USAGE '
log.info '-------------------------------------------------------------'
log.info ''
log.info 'nextflow run iarcbioinfo/RNAseq.nf [-with-docker] --input_folder input/ --ref_folder ref/ [OPTIONS]'
log.info ''
log.info 'Mandatory arguments:'
log.info ' --input_folder FOLDER Folder containing BAM or fastq files to be aligned.'
log.info ' --input_file STRING Input file (tab-separated values) with 4 columns: SM (sample name), RG (read group), pair1 (first fastq pair file), and pair2 (second fastq pair file)'
log.info ' --ref_folder FOLDER Folder with genome reference files (with index).'
log.info ' --gtf FILE Annotation file.'
log.info ' --bed STRING Bed file with interval list'
log.info ""
log.info 'Optional arguments:'
log.info ' --ref FILE Reference fasta file (with index) for splice junction trimming and base recalibration.'
log.info ' --output_folder STRING Output folder (default: .).'
log.info ' --cpu INTEGER Number of cpu used by bwa mem and sambamba (default: 4).'
log.info ' --cpu_gatk INTEGER Number of cpu used by gatk (default: 1).'
log.info ' --cpu_trim INTEGER Number of cpu used by cutadapt (default: 15).'
log.info ' --mem INTEGER Size of memory used for mapping (in GB) (default: 50).'
log.info ' --mem_QC INTEGER Size of memory used for QC and cutadapt (in GB) (default: 2).'
log.info ' --RG STRING Samtools read group specification (default : PL:ILLUMINA).'
log.info ' --STAR_mapqUnique INTEGER STAR default mapping quality for unique mappers (default : 255).'
log.info ' --fastq_ext STRING Extension of fastq files (default : fq.gz)'
log.info ' --suffix1 STRING Suffix of fastq files 1 (default : _1)'
log.info ' --suffix2 STRING Suffix of fastq files 2 (default : _2)'
log.info ' --htseq_maxreads INTEGER Maximum number of reads taken into account by htseq-count (default: htseq-count default=30000000)'
log.info ' --snp_vcf STRING Path to SNP VCF from GATK bundle (default : dbsnp.vcf)'
log.info ' --indel_vcf STRING Path to indel VCF from GATK bundle (default : Mills_1000G_indels.vcf)'
log.info ' --stranded STRING Are reads stranded? (default : no; alternatives : yes, r)'
log.info ' --hisat2_idx STRING hisat2 index file prefix (default : genome_tran)'
log.info ' --multiqc_config STRING Config yaml file for multiqc (default : none)'
log.info ''
log.info 'Flags:'
log.info ' --sjtrim enable splice junction trimming'
log.info ' --recalibration perform base quality score recalibration (GATK)'
log.info ' --hisat2 use hisat2 instead of STAR for reads mapping'
log.info ' --cutadapt perform adapter sequence trimming'
log.info ''
exit 0
}else {
/* Software information */
log.info "input_folder = ${params.input_folder}"
log.info "input_file = ${params.input_file}"
log.info "ref = ${params.ref}"
log.info "cpu = ${params.cpu}"
log.info "cpu_gatk = ${params.cpu_gatk}"
log.info "cpu_trim = ${params.cpu_trim}"
log.info "mem = ${params.mem}"
log.info "mem_QC = ${params.mem_QC}"
log.info "fastq_ext = ${params.fastq_ext}"
log.info "suffix1 = ${params.suffix1}"
log.info "suffix2 = ${params.suffix2}"
log.info "output_folder = ${params.output_folder}"
log.info "bed = ${params.bed}"
log.info "ref_folder = ${params.ref_folder}"
log.info "gtf = ${params.gtf}"
log.info "RG = ${params.RG}"
log.info "STAR_mapqUnique = ${params.STAR_mapqUnique}"
log.info "stranded = ${params.stranded}"
log.info "hisat2_idx = ${params.hisat2_idx}"
log.info "hisat2 = ${params.hisat2}"
log.info "htseq_maxreads = ${params.htseq_maxreads}"
log.info "multiqc_config = ${params.multiqc_config}"
log.info "recalibration = ${params.recalibration}"
log.info "sjtrim = ${params.sjtrim}"
log.info "cutadapt = ${params.cutadapt}"
log.info "snp_vcf = ${params.snp_vcf}"
log.info "indel_vcf = ${params.indel_vcf}"
log.info "help = ${params.help}"
}
suffix2 = params.suffix2
if(suffix2=="null" ) suffix2 = null
//multiqc config file
ch_config_for_multiqc = file(params.multiqc_config)
//read ref files
if(params.hisat2){
ref_1 = Channel.fromPath(params.ref_folder + '/' + params.hisat2_idx + '.1.ht2')
ref_2 = Channel.fromPath(params.ref_folder + '/' + params.hisat2_idx + '.2.ht2')
ref_3 = Channel.fromPath(params.ref_folder + '/' + params.hisat2_idx + '.3.ht2')
ref_4 = Channel.fromPath(params.ref_folder + '/' + params.hisat2_idx + '.4.ht2')
ref_5 = Channel.fromPath(params.ref_folder + '/' + params.hisat2_idx + '.5.ht2')
ref_6 = Channel.fromPath(params.ref_folder + '/' + params.hisat2_idx + '.6.ht2')
ref_7 = Channel.fromPath(params.ref_folder + '/' + params.hisat2_idx + '.7.ht2')
ref_8 = Channel.fromPath(params.ref_folder + '/' + params.hisat2_idx + '.8.ht2')
ref = ref_1.concat( ref_2,ref_3,ref_4,ref_5,ref_6,ref_7,ref_8)
}else{
ref_1 = Channel.fromPath(params.ref_folder +'/chrStart.txt')
ref_2 = Channel.fromPath(params.ref_folder +'/chrNameLength.txt')
ref_3 = Channel.fromPath(params.ref_folder +'/chrName.txt')
ref_4 = Channel.fromPath(params.ref_folder +'/chrLength.txt')
ref_5 = Channel.fromPath(params.ref_folder +'/exonGeTrInfo.tab')
ref_6 = Channel.fromPath(params.ref_folder +'/exonInfo.tab')
ref_7 = Channel.fromPath(params.ref_folder +'/geneInfo.tab')
ref_8 = Channel.fromPath(params.ref_folder +'/Genome')
ref_9 = Channel.fromPath(params.ref_folder +'/genomeParameters.txt')
ref_10 = Channel.fromPath(params.ref_folder +'/SA')
ref_11 = Channel.fromPath(params.ref_folder +'/SAindex')
ref_12 = Channel.fromPath(params.ref_folder +'/sjdbInfo.txt')
ref_13 = Channel.fromPath(params.ref_folder +'/transcriptInfo.tab')
ref_14 = Channel.fromPath(params.ref_folder +'/sjdbList.fromGTF.out.tab')
ref_15 = Channel.fromPath(params.ref_folder +'/sjdbList.out.tab')
ref = ref_1.concat( ref_2,ref_3,ref_4,ref_5,ref_6,ref_7,ref_8,ref_9,ref_10,ref_11,ref_12,ref_13,ref_14,ref_15)
}
gtf = file(params.gtf)
bed = file(params.bed)
//read files
if(params.input_file){
mode = 'infile'
Channel.fromPath("${params.input_file}")
.splitCsv( header: true, sep: '\t', strip: true )
.map { row -> [ row.SM , row.RG , file(row.pair1), file(row.pair2) ] }
.into{ readPairs ; readPairs2}
}else{
mode = 'fastq'
if (file(params.input_folder).listFiles().findAll { it.name ==~ /.*${params.fastq_ext}/ }.size() > 0){
println "fastq files found, proceed with alignment"
}else{
if (file(params.input_folder).listFiles().findAll { it.name ==~ /.*bam/ }.size() > 0){
println "BAM files found, proceed with realignment"; mode ='bam'
files = Channel.fromPath( params.input_folder+'/*.bam' )
.map { path -> [ path.name.replace(".bam",""), "" , path ] }
}else{
println "ERROR: input folder contains no fastq nor BAM files"; System.exit(0)
}
}
}
if(mode=='bam'){
process bam2fastq {
cpus '1'
memory params.mem_QC+'G'
tag { file_tag }
input:
set val(file_tag) , val(rg), file(infile) from files
output:
set val(file_tag), val(file_tag), file("${file_tag}_1.fq.gz"), file("${file_tag}_2.fq.gz") into readPairs0
shell:
file_tag = infile.baseName
'''
set -o pipefail
samtools collate -uOn 128 !{file_tag}.bam tmp_!{file_tag} | samtools fastq -1 !{file_tag}!{params.suffix1}.!{params.fastq_ext} -2 !{file_tag}!{params.suffix2}.!{params.fastq_ext} -
'''
}
readPairs0.into{ readPairs ; readPairs2}
}else{
if(mode=='fastq'){
println "fastq mode"
if(suffix2){
println "paired library"
readPairs0 = Channel.fromFilePairs(params.input_folder +"/*{${params.suffix1},${params.suffix2}}" +'.'+ params.fastq_ext)
.map { row -> [ row[0] , "" , row[1][0], row[1][1] ] }
.view()
.into{ readPairs ; readPairs2}
}else{
println "single library"
readPairs0 = Channel.fromPath(params.input_folder +"/*${params.suffix1}" +'.'+ params.fastq_ext)
.map { row -> [ row.name.replace("${params.suffix1}.${params.fastq_ext}","") , "" , row , file("NO_fastq2") ] }
.view()
.into{ readPairs ; readPairs2}
}
}
}
// pre-trimming QC
process fastqc_pretrim {
cpus params.cpu
memory params.mem_QC+'GB'
tag { file_tag }
input:
set val(file_tag), val(rg), file(pair1) , file(pair2) from readPairs
output:
file("*_pretrim_fastqc.zip") into fastqc_pairs
publishDir "${params.output_folder}/QC/fastq", mode: 'copy', pattern: '{*fastqc.zip}'
shell:
basename1=pair1.name.replace(".${params.fastq_ext}","") //baseName.split("\\.")[0]
basename2=pair2.name.replace(".${params.fastq_ext}","") //baseName.split("\\.")[0]
if(suffix2){
pairs="${pair1} ${pair2}"
}else{
pairs="${pair1}"
}
'''
fastqc -t !{task.cpus} !{pairs}
mv !{basename1}_fastqc.zip !{file_tag}!{params.suffix1}!{rg}_pretrim_fastqc.zip
if [ ! -L NO_fastq2 ]
then mv !{basename2}_fastqc.zip !{file_tag}!{params.suffix2}!{rg}_pretrim_fastqc.zip
fi
'''
}
// adapter sequence trimming and post trimming QC
if(params.cutadapt!=null){
process adapter_trimming {
cpus params.cpu_trim
memory params.mem_QC+'GB'
tag { file_tag +rg }
input:
set val(file_tag), val(rg), file(pair1), file(pair2) from readPairs2
output:
set val(file_tag), val(rg) , file("${file_tag}${rg}*val_1.fq.gz"), file("${file_tag}${rg}*val_2.fq.gz") into readPairs3
file("*_fastqc.zip") into fastqc_postpairs
file("*trimming_report.txt") into trimming_reports
publishDir "${params.output_folder}/QC/adapter_trimming", mode: 'copy', pattern: '{*report.txt,*fastqc.zip}'
shell:
cpu_tg = params.cpu_trim -1
cpu_tg2 = cpu_tg.div(3.5)
cpu_tg3 = Math.round(Math.ceil(cpu_tg2))
if(suffix2){
pairs="${pair1} ${pair2}"
opts="--paired "
}else{
pairs="${pair1}"
opts=" "
}
'''
trim_galore !{opts} --fastqc --gzip --basename !{file_tag}!{rg} -j !{cpu_tg3} !{pairs}
if [ -L NO_fastq2 ]
mv !{file_tag}!{rg}_trimmed.fq.gz !{file_tag}!{rg}_val_1.fq.gz
then touch !{file_tag}!{rg}_val_2.fq.gz
fi
'''
}
}else{
readPairs3 = readPairs2
fastqc_postpairs=Channel.empty()
trimming_reports=Channel.empty()
}
readPairs_align = readPairs3.groupTuple(by: 0)
//Mapping, mark duplicates and sorting
process alignment {
cpus params.cpu
memory params.mem+'G'
tag { file_tag }
input:
set val(file_tag), val(rg), file(pair1), file(pair2) from readPairs_align
file ref from ref.collect()
file gtf
output:
set val(file_tag), val(rg) , file("${file_tag}.bam"), file("${file_tag}.bam.bai") into bam_files
file("*Log*") into align_out
set val(file_tag), file("*SJ.out.junction") into SJ_out
file("*SJ.out.tab") into SJ_out_others
if( (params.sjtrim == null)&&(params.recalibration == null) ){
publishDir params.output_folder, mode: 'copy', saveAs: {filename ->
if (filename.indexOf(".bam") > 0) "BAM/$filename"
else if (filename.indexOf("SJ") > 0) "BAM/$filename"
//else if (filename.indexOf("Log") > 0) "QC/alignment/$filename"
}
}else{
publishDir params.output_folder, mode: 'copy', saveAs: {filename ->
if (filename.indexOf("SJ") > 0) "BAM/$filename"
//else if (filename.indexOf("Log") > 0) "QC/alignment/$filename"
}
}
shell:
align_threads = params.cpu.intdiv(2)
sort_threads = params.cpu.intdiv(2) - 1
sort_mem = params.mem.intdiv(4)
input_f1="${pair1[0]}"
rgtmp="${rg[0]}"
if(rgtmp=="") rgtmp="${file_tag}"
rgline="ID:${rgtmp} SM:${file_tag} ${params.RG}"
for( p1tmp in pair1.drop(1) ){
input_f1=input_f1+",${p1tmp}"
}
for( rgtmp in rg.drop(1) ){
if(rgtmp=="") rgtmp="${file_tag}"
rgline=rgline+" , ID:${rgtmp} SM:${file_tag} ${params.RG}"
}
if(suffix2){
input_f2="${pair2[0]}"
for( p2tmp in pair2.drop(1) ){
input_f2=input_f2+",${p2tmp}"
}
pairs="${input_f1} ${input_f2}"
}else{
pairs="${input_f1}"
}
'''
STAR --outSAMattrRGline !{rgline} --outSAMmapqUnique !{params.STAR_mapqUnique} --chimSegmentMin 12 --chimJunctionOverhangMin 12 \
--chimSegmentReadGapMax 3 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 \
--alignSJstitchMismatchNmax 5 -1 5 5 --outSAMstrandField intronMotif --chimMultimapScoreRange 10 --chimMultimapNmax 10 \
--chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --chimOutJunctionFormat 1 --twopassMode Basic \
--outReadsUnmapped None --runThreadN !{align_threads} --genomeDir . --sjdbGTFfile !{gtf} --readFilesCommand zcat \
--readFilesIn !{pairs} --outStd SAM | samblaster --addMateTags | sambamba view -S -f bam -l 0 /dev/stdin | sambamba sort -t !{sort_threads} -m !{sort_mem}G --tmpdir=!{file_tag}_tmp -o !{file_tag}.bam /dev/stdin
mv Chimeric.out.junction STAR.!{file_tag}.Chimeric.SJ.out.junction
mv SJ.out.tab STAR.!{file_tag}.SJ.out.tab
mv Log.final.out STAR.!{file_tag}.Log.final.out
mv Log.out STAR.!{file_tag}.Log.out
mv Log.progress.out STAR.!{file_tag}.Log.progress.out
mv Log.std.out STAR.!{file_tag}.Log.std.out
'''
}
fasta_ref = file(params.ref)
fasta_ref_fai = file(params.ref + '.fai')
if( (params.sjtrim!=null)||(params.recalibration!=null) ){
fasta_ref_dictn = params.ref[0..<params.ref.lastIndexOf('.')]
fasta_ref_dict = file(fasta_ref_dictn + '.dict')
}
//Splice junctions trimming
if(params.sjtrim){
process splice_junct_trim {
cpus params.cpu_gatk
memory params.mem+'G'
tag { file_tag }
input:
set val(file_tag), val(rg), file(bam), file(bai) from bam_files
file fasta_ref
file fasta_ref_fai
file fasta_ref_dict
output:
set val(file_tag_new), val(rg), file("${file_tag_new}.bam"), file("${file_tag_new}.bam.bai") into bam_files2
if(params.recalibration == null){
publishDir "${params.output_folder}/BAM", mode: 'copy'
}
shell:
file_tag_new = file_tag+'_split'
'''
gatk SplitNCigarReads --java-options "-Xmx!{params.mem}G" -R !{fasta_ref} -I !{bam} -O !{file_tag_new}.bam
mv !{file_tag_new}.bai !{file_tag_new}.bam.bai
'''
}
}else{
bam_files2=bam_files
}
//BQSrecalibration GATK4
if(params.recalibration){
//get know site VCFs from GATK bundle
known_snps = file( params.snp_vcf )
known_snps_index = file( params.snp_vcf+'.tbi' )
known_indels = file( params.indel_vcf )
known_indels_index = file( params.indel_vcf+'.tbi' )
process base_quality_score_recalibration {
cpus params.cpu_gatk
memory params.mem+'G'
tag { file_tag }
publishDir "$params.output_folder/BAM/", mode: 'copy', pattern: "*bam*"
publishDir "$params.output_folder/QC/BAM/BQSR/", mode: 'copy',
saveAs: {filename ->
if (filename.indexOf("table") > 0) "$filename"
else if (filename.indexOf("plots") > 0) "$filename"
else null
}
input:
set val(file_tag), val(rg), file("${file_tag}.bam"), file("${file_tag}.bam.bai") from bam_files2
file known_snps
file known_snps_index
file known_indels
file known_indels_index
file fasta_ref
file fasta_ref_fai
file fasta_ref_dict
output:
file("*_recal.table") into recal_table_files
file("*plots.pdf") into recal_plots_files
set val(file_tag_new), val(rg), file("${file_tag_new}.bam"), file("${file_tag_new}.bam.bai") into recal_bam_files
shell:
file_tag_new=file_tag+'_BQSRecalibrated'
'''
gatk BaseRecalibrator --java-options "-Xmx!{params.mem}G" -R !{fasta_ref} -I !{file_tag}.bam --known-sites !{known_snps} --known-sites !{known_indels} -O !{file_tag}_recal.table
gatk ApplyBQSR --java-options "-Xmx!{params.mem}G" -R !{fasta_ref} -I !{file_tag}.bam --bqsr-recal-file !{file_tag}_recal.table -O !{file_tag_new}.bam
gatk BaseRecalibrator --java-options "-Xmx!{params.mem}G" -R !{fasta_ref} -I !{file_tag_new}.bam --known-sites !{known_snps} --known-sites !{known_indels} -O !{file_tag_new}_recal.table
gatk AnalyzeCovariates --java-options "-Xmx!{params.mem}G" -before !{file_tag}_recal.table -after !{file_tag_new}_recal.table -plots !{file_tag_new}_recalibration_plots.pdf
mv !{file_tag_new}.bai !{file_tag_new}.bam.bai
'''
}
}else{
recal_bam_files=bam_files2
}
recal_bam_files.into { recal_bam_files4QC; recal_bam_files4quant ; recal_bam4QCsplittmp }
//RSEQC
process RSEQC{
cpus '1'
memory params.mem_QC+'GB'
tag { file_tag }
input:
set val(file_tag), val(rg), file(bam), file(bai) from recal_bam_files4QC
file bed
output:
file("${file_tag}_readdist.txt") into rseqc_files
file("*clipping*") into rseqc_clip_files
file("*jun_saturation*") into rseqc_jsat_files
publishDir "${params.output_folder}/QC/bam", mode: 'copy'
shell:
'''
read_distribution.py -i !{bam} -r !{bed} > !{file_tag}"_readdist.txt"
clipping_profile.py -i !{bam} -s "PE" -o !{file_tag}"_clipping"
junction_saturation.py -i !{bam} -r !{bed} -o !{file_tag}"_jun_saturation"
'''
}
simple = Channel.create()
recal_bam_files4QCsplit0 = Channel.create()
recal_bam_files4QCsplit = Channel.create()
recal_bam_files4QCsplit4test = Channel.create()
recal_bam4QCsplittmp.choice( simple,recal_bam_files4QCsplit0 ) { a -> a[1].size() == 1 ? 0 : 1 }
recal_bam_files4QCsplit0.into( recal_bam_files4QCsplit , recal_bam_files4QCsplit4test)
process RSEQCsplit{
cpus '1'
memory params.mem_QC+'GB'
tag { file_tag }
input:
set val(file_tag), val(rg), file(bam), file(bai) from recal_bam_files4QCsplit
file bed
output:
file("*readdist.txt") into rseqc_files_split
publishDir "${params.output_folder}/QC/bam", mode: 'copy'
shell:
basename = bam.baseName
'''
samtools split !{bam} -f "%*_%!.%."
for f in `ls !{basename}_*.bam`;
do read_distribution.py -i $f -r !{bed} > ${f%.bam}"_readdist.txt";
done
'''
}
if( recal_bam_files4QCsplit4test.ifEmpty(0)==0 ){
recal_bam_files4QCsplit4test.subscribe { row -> println "${row}" }
println("No files to split")
rseqc_files_split = Channel.empty()
}
//Quantification
process quantification{
cpus params.cpu
if( (params.sjtrim)||(params.recalibration) ){
memory params.mem+'GB'
}else{
memory params.mem_QC+'GB'
}
tag { file_tag }
input:
set val(file_tag), val(rg), file(bam), file(bai) from recal_bam_files4quant
file gtf
output:
file("${file_tag}_count.txt") into htseq_files
publishDir "${params.output_folder}/counts", mode: 'copy'
shell:
buffer=''
if(params.htseq_maxreads) buffer='--max-reads-in-buffer '+params.htseq_maxreads
if( (params.sjtrim)||(params.recalibration) ){
'''
mv !{file_tag}.bam !{file_tag}_coordinate_sorted.bam
sambamba sort -n -t !{task.cpus} -m !{params.mem}G --tmpdir=!{file_tag}_tmp -o !{file_tag}.bam !{file_tag}_coordinate_sorted.bam
htseq-count -n !{params.cpu} -r name -s !{params.stranded} -f bam !{file_tag}.bam !{gtf} !{buffer} --additional-attr=gene_name > !{file_tag}_count.txt
'''
}else{
'''
htseq-count -n !{params.cpu} -r pos -s !{params.stranded} -f bam !{file_tag}.bam !{gtf} !{buffer} --additional-attr=gene_name > !{file_tag}_count.txt
'''
}
}
process multiqc_pretrim {
cpus '1'
memory params.mem_QC+'GB'
tag { "all"}
input:
file fastqc1 from fastqc_pairs.collect()
file multiqc_config from ch_config_for_multiqc
output:
file("multiqc_pretrim_report.html") into multiqc_pre
file("multiqc_pretrim_report_data") into multiqc_pre_data
publishDir "${params.output_folder}/QC", mode: 'copy'
shell:
if( multiqc_config.name=='NO_FILE' ){
opt = ""
}else{
opt = "--config ${multiqc_config}"
}
'''
for f in $(find *fastqc.zip -type l);do cp --remove-destination $(readlink $f) $f;done;
multiqc . -n multiqc_pretrim_report.html -m fastqc !{opt} --comment "RNA-seq Pre-trimming QC report"
'''
}
process multiqc_posttrim {
cpus '1'
memory params.mem_QC+'GB'
tag { "all"}
input:
file STAR from align_out.collect()
file htseq from htseq_files.collect()
file rseqc_clip from rseqc_clip_files.collect()
file rseqc from rseqc_files.collect()
file rseqc_jsat from rseqc_jsat_files.collect()
file trim from trimming_reports.collect().ifEmpty([])
file fastqcpost from fastqc_postpairs.collect().ifEmpty([])
file rseqc_split from rseqc_files_split.collect().ifEmpty([])
file multiqc_config from ch_config_for_multiqc
output:
file("multiqc_posttrim_report.html") into multiqc_post
file("multiqc_posttrim_report_data") into multiqc_post_data
publishDir "${params.output_folder}/QC", mode: 'copy'
shell:
if( multiqc_config.name=='NO_FILE' ){
opt = ""
}else{
opt = "--config ${multiqc_config}"
}
'''
if $(compgen -G "*fastq.zip" > /dev/null); then for f in $(find *fastqc.zip -type l);do cp --remove-destination $(readlink $f) $f;done; fi;
multiqc . -n multiqc_posttrim_report.html -m fastqc -m cutadapt -m star -m rseqc -m htseq !{opt} --comment "RNA-seq Post-trimming QC report"
'''
}