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main.nf
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nextflow.enable.dsl=2
// Project Params:
params.sheet = "sample-sheet.csv"
params.reads = "$workDir/fastqs/*_*{1,2}.f*.gz"
// Module Params:
params.help = false
params.listGenomes = false
params.bwa = false
params.bowtie2 = false
params.fastp = false
// Default Params:
params.mode = "PE"
params.id = "TREx_ID"
params.fecutoff = 5
params.qval = 0.05
params.genome = null
params.bg = null
// Command Line Channels ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
ch_pin = channel.value(params.id)
ch_sheet = channel.fromPath(params.sheet)
ch_qval = channel.value(params.qval)
ch_fe = channel.value(params.fecutoff)
ch_mqc_conf = channel.fromPath("${projectDir}/multiqc_config.yaml")
ch_mqc_logo = channel.fromPath("${projectDir}/img/trex-mini.png")
// ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
if( params.help ) {
log.info """
A T A C - S E Q W O R K F L O W - @bixBeta
=======================================================================================================================================================================
Usage:
nextflow run https://github.com/bixbeta/atac -r main < args ... >
Args:
* --help : Prints this help documentation
* --listGenomes : Get extended list of genomes available for this pipeline
* --id : TREx Project ID
* --sheet : sample-sheet.csv < default: looks for a file named sample-sheet.csv in the project dir >
-------------------------------------------
Sample Sheet Example:
label fastq1 fastq2
SS1 SS1_R1.fastq.gz SS1_R2.fastq.gz
SS2 SS2_R1.fastq.gz SS2_R2.fastq.gz
.
.
. etc.
-------------------------------------------
* --bwa : deprecated
* --bowtie2 : invokes bowtie2 alignment step
* --fastp : invokes fastp trimming
* --mode : PE (default)
* --fecutoff : 5 (default)
* --qval : 0.05 (default)
* --genome : reference genome ( Available genomes: hg38, mm10 & dm6 : Use --listGenomes for more details )
* --bg : Input Control Sample ID
"""
exit 0
}
// BT2 Indices MAP
genomeDir = [
mm10 :"/workdir/genomes/Mus_musculus/mm10/ENSEMBL/bowtie2index",
hg38 :"/workdir/genomes/Homo_sapiens/hg38/ENSEMBL/BT2.ENSEMBL_INDEX",
dm6 :"/workdir/genomes/Drosophila_melanogaster/dm6/ENSEMBL/Bowtie2.Index"
]
bt2Prefix = [
mm10 :"/mm10",
hg38 :"/hg38",
dm6 :"/dm6"
]
gAlias = [
mm10 :"mouse",
hg38 :"human",
dm6 :"fly"
]
gtfs = [
mm10 :"/workdir/genomes/Mus_musculus/mm10/ENSEMBL/Mus_musculus.GRCm38.96.gtf",
hg38 :"/workdir/genomes/Homo_sapiens/hg38/ENSEMBL/Homo_sapiens.GRCh38.96.gtf",
dm6 :"/workdir/genomes/Drosophila_melanogaster/dm6/ENSEMBL/Drosophila_melanogaster.BDGP6.32.106.gtf"
]
blkList = [
mm10 :"/workdir/genomes/Mus_musculus/mm10/ENSEMBL/no-chr-mm10-blacklist.v2.bed",
hg38 :"/workdir/genomes/Homo_sapiens/hg38/ENSEMBL/no-chr-hg38-blacklist.v2.bed",
dm6 :"/workdir/tools/blacklists/dm6-blacklist.v2.bed"
]
gSize = [
mm10 :"mm",
hg38 :"hs",
dm6 :"dm"
]
bwgSize = [
mm10 :2652783500,
hg38 :2913022398,
dm6 :142573017
]
if( params.listGenomes) {
println("")
log.info """
Available BT2 Indices
=========================================================================================================================
"""
.stripIndent()
printMap = { a, b -> println "$a ----------- $b" }
genomeDir.each(printMap)
log.info """
gtfs
=========================================================================================================================
"""
.stripIndent()
printMap = { a, b -> println "$a ----------- $b" }
gtfs.each(printMap)
log.info """
blackLists
=========================================================================================================================
"""
.stripIndent()
printMap = { a, b -> println "$a ----------- $b" }
blkList.each(printMap)
exit 0
}
// Load all modules
include { FASTP } from './modules/fastp'
include { BOWTIE2 } from './modules/bowtie2'
include { MTBLKDUP } from './modules/bowtie2'
include { TAGDIR } from './modules/homer'
include { MACS2; NObgMACS2 } from './modules/macs2'
include { MACS2ALL; NObgMACS2ALL } from './modules/macs2'
include { FRIP; NObgFRIP } from './modules/macs2'
include { BIGWIG } from './modules/deeptools'
include { RSYNC } from './modules/deeptools'
include { MQC } from './modules/multiqc'
include { MQC2 } from './modules/multiqc'
// BOWTIE2 WORKFLOW:
workflow BTPAIRED {
meta_ch = ch_sheet
| splitCsv( header:true )
| map { row -> [row.label, [file("fastqs/" + row.fastq1), file("fastqs/" + row.fastq2)]] }
| view
if( params.fastp ){
FASTP(meta_ch)
.set { fastp_out }
} else {
fastp_out = meta_ch
}
genome = genomeDir[params.genome]
ch_genome = channel.value(genome)
genome_prefix = bt2Prefix[params.genome]
ch_genome_prefix = channel.value(genome_prefix)
ch_alias = channel.value(gAlias[params.genome])
ch_gtf = channel.value(gtfs[params.genome])
ch_blkList = channel.value(blkList[params.genome])
ch_gsize = channel.value(gSize[params.genome])
ch_bwg_size = channel.value(bwgSize[params.genome])
if( params.bowtie2){
BOWTIE2(fastp_out, ch_genome, ch_genome_prefix)
MTBLKDUP(BOWTIE2.out.primary_sorted_bam,
BOWTIE2.out.primary_sorted_bai,
ch_blkList)
TAGDIR(MTBLKDUP.out.dedup_bam)
BIGWIG(MTBLKDUP.out.dedup_bam, MTBLKDUP.out.dedup_bai, ch_bwg_size)
// RSYNC(BIGWIG.out.big_wig)
// RSYNC.out.ftp_path.collect().view()
if(params.bg != null){
ch_dedup_bams = MTBLKDUP.out.dedup_bam
.view()
ch_bg = ch_dedup_bams
.filter{ it[0] == params.bg}
.collect()
.view()
//ch_bg_val = channel.value(ch_bg)
ch_atac_bams = ch_dedup_bams
.filter{ it[0] != params.bg}
MACS2(ch_atac_bams, ch_bg , ch_qval, ch_fe, ch_gsize)
ch_atac_bams_all = ch_atac_bams
.map({ it -> it[1]}).collect()
.view()
MACS2ALL(ch_atac_bams_all, ch_bg , ch_qval, ch_fe, ch_gsize, ch_genome, ch_gtf)
ch_saf = MACS2ALL.out.saf.collect().view()
FRIP(ch_atac_bams, ch_saf)
ch2_mqc = FRIP.out.raw_counts_summary
.collect()
.view()
MQC2(ch2_mqc, ch_mqc_conf, ch_mqc_logo)
} else {
ch_dedup_bams = MTBLKDUP.out.dedup_bam
.view()
NObgMACS2(ch_dedup_bams, ch_qval, ch_fe, ch_gsize)
ch_atac_bams_all = ch_dedup_bams
.map({ it -> it[1]}).collect()
.view()
NObgMACS2ALL(ch_atac_bams_all, ch_qval, ch_fe, ch_gsize, ch_genome, ch_gtf)
ch_saf = NObgMACS2ALL.out.saf.collect().view()
NObgFRIP(ch_dedup_bams, ch_saf)
ch2_mqc = NObgFRIP.out.raw_counts_summary
.collect()
.view()
MQC2(ch2_mqc, ch_mqc_conf, ch_mqc_logo)
}
}
if( params.genome != null ){
ch1_mqc = BOWTIE2.out.primary_log
.concat(BOWTIE2.out.primary_flagstat)
.concat(BOWTIE2.out.primary_idxstats)
// .concat(MTBLKDUP.out.nomt_flagstat)
// .concat(MTBLKDUP.out.nomt_idxstats)
.concat(MTBLKDUP.out.nomt_nobl_dupmarked_flagstat)
.concat(MTBLKDUP.out.nomt_nobl_dupmarked_idxstats)
.concat(MTBLKDUP.out.dup_stats)
.concat(MTBLKDUP.out.dedup_flagstat)
.concat(MTBLKDUP.out.dedup_idxstats)
.collect()
.view()
MQC(ch1_mqc, ch_mqc_conf, ch_mqc_logo)
}
}
workflow {
if (params.mode == "PE" ) {
BTPAIRED()
} else {
error "Invalid Workflow"
exit 0
}
}