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main.nf
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nextflow.enable.dsl=2
// Project Params:
params.sheet = "sample-sheet.csv"
params.outdir = "$projectDir/STAR_OUT"
params.reads = "$workDir/fastqs/*_*{1,2}.f*.gz"
// Module Params:
params.help = false
params.listGenomes = false
params.gbcov = false
params.screen = false
params.fastp = false
// Defaule Params:
params.mode = "PE"
params.id = "TREx_ID"
params.strand = 2
params.chromosub = "10"
params.genome2 = null
params.genome = null
params.splitname = "na"
runmode = params.mode
pin = channel.value(params.id)
if( params.help ) {
log.info """
R N A - S E Q W O R K F L O W - @bixBeta
=======================================================================================================================================================================
Usage:
nextflow run https://github.com/bixbeta/nextflow -r main < args ... >
Args:
* --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.
-------------------------------------------
* --mode : use 'PE' for paired end data; default <PE>
: use 'PES' for paired end data + split unmapped
: use 'PEBS' for paired end bacterial data + split unmapped
: use 'SE' for single end data
: use 'SES' for single end data + split unmapped
: use 'SEBS' for single end bacterial data + split unmapped
* --strand : 0,1 or 2 for unstranded, first-strand and second-strand; default <2>
* --fastp : Invokes fastp trimming module.
* --genome : Genome index. Use --listGenomes flag to see all available genomes. Also supports a path value for starIndex dir.
* --genome2 : Secondary Genome index. This will align the --genome subtracted reads to --genome2 index.
* --screen : Invokes the fastq_screen step. See the screen.conf file here <https://github.com/bixBeta/nextflow/blob/main/screen.conf> for more details.
* --gbcov : Runs GeneBodyCoverage Program on sub-setted bams.
* --chromosub : Subset bams to specified chromosome name. < defaults to chromosome 10 >
* --splitname : A string that will be used to denote --genome2 e.g. "GRC100011A", "Cat_custom" etc.
"""
exit 0
}
log.info """
R N A - S E Q W O R K F L O W - @bixBeta
=========================================================================================================================
trexID : ${params.id}
reads : ${params.reads}
fastp : ${params.fastp}
genome : ${params.genome}
mode : ${params.mode}
genome2 : ${params.genome2}
screen : ${params.screen}
gbcov : ${params.gbcov}
chromosub : ${params.chromosub}
splitname : ${params.splitname}
"""
// STAR index MAP
genomeDir = [
hg38 :"/workdir/genomes/Homo_sapiens/hg38/UCSC/hg38.star",
mm10 :"/workdir/genomes/Mus_musculus/mm10/UCSC/mm10.star",
GRCh38 :"/workdir/genomes/Homo_sapiens/hg38/ENSEMBL/GRCh38.star",
GRCm38 :"/workdir/genomes/Mus_musculus/mm10/ENSEMBL/GRCm38.star",
cat :"/workdir/genomes/Felis_catus/Felis_catus9.0/Ensembl/genomeDir",
chicken :"/workdir/genomes/Gallus_gallus/Galgal5/ENSEMBL/galgal5.star",
chicken6 :"/workdir/genomes/Gallus_gallus/Galgal6/ENSEMBL/gtf.102/star.index.102",
horse :"/workdir/genomes/Equus_caballus/EquCab3/ENSEMBL/genebuild-102/star.index.102",
horse2 :"/workdir/genomes/Equus_caballus/EquCab2/ENSEMBL/EquCab2.star.index",
ATCC_13047 :"/workdir/genomes/Enterobacter_cloacae/ATCC_13047/custom/ATCC_13047.GTF",
grape :"/workdir/genomes/Vitis_vinifera/GCA_000003745.2/ENSEMBL/Vitis_vinifera.12X.43.bed12",
rat :"/workdir/genomes/Rattus_norvegicus/rn6/ENSEMBL/rat.star",
ercc :"/workdir/genomes/contaminants/ERCC_spikeIns/ercc.star",
lonchura :"/workdir/genomes/Lonchura_striata/LonStrDom1/ENSEMBL/lonchura.star",
goose :"/workdir/genomes/Anser_brachyrhynchus/ASM259213v1/ENSEMBL/goose.star",
ehv8 :"/workdir/genomes/FastQ_Screen_Genomes/EHV8/ehv8.star",
erdman :"/workdir/genomes/Mycobacterium_tuberculosis/Erdman_GCA_000350205.1/ENSEMBL/genomeDir",
TB :"/workdir/genomes/Mycobacterium_tuberculosis/CDC1551_Ensembl/cdc1551.star",
TB2 :"/workdir/genomes/Mycobacterium_tuberculosis/Ensembl_GCA_000668235/GCA_000668235.star",
maize4 :"/workdir/genomes/Zea_mays/B73_RefGen_v4/ENSEMBL/star.maize",
maize3 :"/workdir/genomes/Zea_mays/B73_RefGen_v3/NCBI/genomeDir",
finch :"/workdir/genomes/Taeniopygia_guttata/taeGut3.2.4/ENSEMBL/UPDATED.ANNOTS/star.index.updated",
finch2 :"/workdir/genomes/Geospiza_fortis_ground_finch/GeoFor_1.0/NCBI/star.index",
green :"/workdir/genomes/Chlorocebus_sabaeus/CHlSab1/ENSEMBL/genomeDir",
dog :"/workdir/genomes/Canis_familiaris/canFam3/ENSEMBL/CanFam3.1.101/genomeDir",
faba :"/workdir/genomes/Vicia_faba/VfEP_Reference-Unigene/NCBI/genomeDir-wo-gff",
aphid :"/workdir/genomes/Acyrthosiphon_pisum/pea_aphid_22Mar2018_4r6ur/NCBI/genomeDir",
cholera :"/workdir/genomes/Vibrio_cholerae/N16961/NCBI/genomeDir",
BG8 :"/workdir/genomes/Methylomicrobium_album_BG8/ASM21427v3/NCBI/custom3-CDS2exon/genomeDir_fixSpaces",
aedes :"/workdir/genomes/Aedes_aegypti/AaegL5.0/NCBI/AaegL5.0.star",
aedesVB :"/workdir/genomes/Aedes_aegypti/AaegL5.0/Vectorbase/AaegyptiLVP_AGWG_release49/genomeDir.vectorBase",
DC3000c :"/workdir/genomes/Pseudomonas_syringae/Tomato_DC3000/Custom_Zichu/starIndex_8.gtf_simplenames",
Theileria :"/workdir/genomes/Theileria/Tannulata_ASM322v1/NCBI/starIndex",
cow :"/workdir/genomes/Bos_taurus/ARS-UCD1.2_GCA_002263795.2/ENSEMBL/star.index",
salmonella :"/workdir/genomes/Salmonella_enterica/ASM21085v2/NCBI/genomeDir",
salmonella2 :"/workdir/genomes/Salmonella_enterica/ASM2216v1/NCBI/genomeDir",
EA273 :"/workdir/genomes/Erwinia_amylovora/GCF_000091565.1/ncbi/genomeDir",
ddSmed :"/workdir/genomes/Schmidtea_mediterranea/dd_Smed_v6/NCBI/genomeDir",
yeast :"/workdir/genomes/Saccharomyces_cerevisiae/R64-1-1_GCA_000146045.2/ENSEMBL/star.index",
arabidopsis :"/workdir/genomes/Arabidopsis_thaliana/TAIR10/ENSEMBL/genomeDir",
crow :"/workdir/genomes/Corvus_moneduloides/bCorMon1/NCBI/genomeDir",
orbicella :"/workdir/genomes/Orbicella_faveolata/GCA_002042975.1/ncbi/genomeDir",
bacillus :"/workdir/genomes/Bacillus_subtilis/GCA_000009045/ENSEMBL/genomeDir",
pao1 :"/workdir/genomes/Pseudomonas_aeruginosa/PAO1/NCBI/genomeDir",
grape :"/workdir/genomes/Vitis_vinifera/GCA_000003745.2/ENSEMBL/Vitis_vinifera.star",
cowUMD :"/workdir/genomes/Bos_taurus/UMD_3.1.1/NCBI/genomeDir/",
guppy :"/workdir/genomes/Poecilia_reticulata/GCF_000633615.1/NCBI/genomeDir",
dm6 :"/workdir/genomes/Drosophila_melanogaster/dm6/ENSEMBL/genomeDir",
tomato :"/workdir/genomes/Solanum_lycopersicum/custom/genomeDir",
macaca :"/workdir/genomes/Macaca_fascicularis/GCF_000364345.1_Macaca_fascicularis_5.0/NCBI/genomeDir",
triticum :"/workdir/genomes/Triticum_aestivum/IWGSC_CS_RefSeq-v2-1/NCBI/genomeDir",
cassava :"/workdir/genomes/Manihot_esculenta_Cassava/Mesculenta_v8/NCBI/genomeDir",
gluconobacter :"/workdir/genomes/Gluconobacter_oxydans/GCF_020180925.1/NCBI/genomeDir",
calypte :"/workdir/genomes/Calypte_anna/GCF_003957555.1_bCalAnn1_v1.p/NCBI/genomeDir/"]
// BED12's for RSEQC geneBody coverage process
bed12 = [
hg38 :"/workdir/genomes/Homo_sapiens/hg38/UCSC/genes.bed12",
mm10 :"/workdir/genomes/Mus_musculus/mm10/UCSC/BED12/mm10.ucsc.bed12",
GRCh38 :"/workdir/genomes/Homo_sapiens/hg38/ENSEMBL/Homo_sapiens.GRCh38.bed12",
GRCm38 :"/workdir/genomes/Mus_musculus/mm10/ENSEMBL/Mus_musculus.GRCm38.bed12",
cat :"/workdir/genomes/Felis_catus/Felis_catus9.0/Ensembl/Felis_catus.Felis_catus_9.0.95.bed12",
chicken :"/workdir/genomes/Gallus_gallus/Galgal5/ENSEMBL/Gallus_gallus.Gallus_gallus-5.0.bed12",
chicken6 :"/workdir/genomes/Gallus_gallus/Galgal6/ENSEMBL/gtf.102/Gallus_gallus.GRCg6a.102.bed12",
horse :"/workdir/genomes/Equus_caballus/EquCab3/ENSEMBL/genebuild-102/Equus_caballus.EquCab3.0.102.bed12",
horse2 :"/workdir/genomes/Equus_caballus/EquCab2/ENSEMBL/Equus_caballus.EquCab2.94.BED12",
ATCC_13047 :"/workdir/genomes/Enterobacter_cloacae/ATCC_13047/GCF_000025565.1_ASM2556v1_genomic.bed12",
grape :"/workdir/genomes/Vitis_vinifera/GCA_000003745.2/ENSEMBL/Vitis_vinifera.star",
rat :"/workdir/genomes/Rattus_norvegicus/rn6/ENSEMBL/Rattus_norvegicus.Rnor_6.0.bed12",
lonchura :"/workdir/genomes/Lonchura_striata/LonStrDom1/ENSEMBL/Lonchura_striata_domestica.LonStrDom1.bed12",
goose :"/workdir/genomes/Anser_brachyrhynchus/ASM259213v1/ENSEMBL/Anser_brachyrhynchus.ASM259213v1.bed12",
maize4 :"/workdir/genomes/Zea_mays/B73_RefGen_v4/ENSEMBL/Zea_mays.B73_RefGen_v4.bed12",
finch :"/workdir/genomes/Taeniopygia_guttata/taeGut3.2.4/ENSEMBL/UPDATED.ANNOTS/Taeniopygia_guttata.bTaeGut1_v1.p.bed12",
finch2 :"/workdir/genomes/Geospiza_fortis_ground_finch/GeoFor_1.0/NCBI/GCF_000277835.1_GeoFor_1.0_genomic.bed12",
dog :"/workdir/genomes/Canis_familiaris/canFam3/ENSEMBL/CanFam3.1.101/Canis_lupus_familiaris.CanFam3.1.101.bed12",
aedes :"/workdir/genomes/Aedes_aegypti/AaegL5.0/NCBI/GCF_002204515.2_AaegL5.0_genomic.bed12",
aedesVB :"/workdir/genomes/Aedes_aegypti/AaegL5.0/Vectorbase/AaegyptiLVP_AGWG_release49/VectorBase-49_AaegyptiLVP_AGWG.BED12",
cow :"/workdir/genomes/Bos_taurus/ARS-UCD1.2_GCA_002263795.2/ENSEMBL/Bos_taurus.ARS-UCD1.2.BED12",
BG8 :"/workdir/genomes/Methylomicrobium_album_BG8/ASM21427v3/NCBI/test/ncbi-genomes-2020-08-27/GCF_000214275.2_ASM21427v3_genomic.bed12",
ddSmed :"/workdir/genomes/Schmidtea_mediterranea/dd_Smed_v6/NCBI/dd_Smed_v6.pcf.bed12",
cowUMD :"/workdir/genomes/Bos_taurus/UMD_3.1.1/NCBI/GCF_000003055.6_Bos_taurus_UMD_3.1.1_genomic.bed12",
dm6 :"/workdir/genomes/Drosophila_melanogaster/dm6/ENSEMBL/Drosophila_melanogaster.BDGP6.32.bed12",
tomato :"/workdir/genomes/Solanum_lycopersicum/custom/ITAG4.0_gene_models.bed12",
yeast :"/workdir/genomes/Saccharomyces_cerevisiae/R64-1-1_GCA_000146045.2/ENSEMBL/Saccharomyces_cerevisiae.R64-1-1.bed12"]
// genomeKey.list = (genomeDir.collectMany{ k,v -> (v == params.genome) ? [k] : []} as String[])
// genomeKey = genomeKey.list[0]
if( params.listGenomes) {
println("")
log.info """
Available STAR Indices
=========================================================================================================================
"""
.stripIndent()
printMap = { a, b -> println "$a ----------- $b" }
genomeDir.each(printMap)
log.info """
BED12's for GeneBodyCov Process
=========================================================================================================================
"""
.stripIndent()
printMap = { a, b -> println "$a ----------- $b" }
bed12.each(printMap)
exit 0
}
include { FASTPM } from './modules/fastp'
include { STARM ; COUNTSM } from './modules/star'
include { GBCOV1M ; GBCOV2M } from './modules/gbcov'
include { STARM2 ; COUNTSM2 } from './modules/realign'
include { MQC ; MQC2 ; MQCSCREENM } from './modules/multiqc'
include { SCREENM } from './modules/screen'
ch_sheet = channel.fromPath(params.sheet)
ch_mqc_conf = channel.fromPath("${projectDir}/multiqc_config.yaml")
ch_mqc_logo = channel.fromPath("${projectDir}/img/trex-extended-logo.png")
ch_screen_conf = channel.value("${projectDir}/screen.conf")
splitName = params.splitname
if (genomeDir.containsKey(params.genome)){ // allows a user to pass a STAR index path via --genome parameter
genome = genomeDir[params.genome]
} else {
genome = params.genome
}
genome_ch = channel.value(genome)
// genome_key_ch = channel.value(params.genome)
if (bed12.containsKey(params.genome)){ // allows a user to pass a STAR index path via --genome parameter
bed = bed12[params.genome]
} else {
bed = null
}
bed_ch = channel.value(bed)
if (genomeDir.containsKey(params.genome2)){ // allows a user to pass a STAR index path via --genome parameter
genome2 = genomeDir[params.genome2]
splitName_ch = channel.value(params.genome2)
} else {
genome2 = params.genome2
splitName_ch = channel.value(params.splitname)
}
genome_ch2 = channel.value(genome2)
/* ---------------------------------------------------------------------------------------------------------
SINGLE END NOVA/NEXT-seq Workflow
------------------------------------------------------------------------------------------------------------ */
workflow SINGLE {
meta_ch = ch_sheet
| splitCsv( header:true )
| map { row -> [row.label, [file("fastqs/" + row.fastq1)]] }
| view
if(params.fastp){
FASTPM(meta_ch)
.set { fastp_out }
} else {
fastp_out = meta_ch
}
if( params.genome != null ){
STARM(fastp_out, genome_ch)
bam_ch = STARM.out.bam_sorted
| collect
| flatten
unmapped_ch = STARM.out.unmapped
// chromo_sub = channel.value(params.gbcov)
chromo_sub = channel.value(params.chromosub)
}
if( params.screen ) {
SCREENM(fastp_out, ch_screen_conf)
screen_out_ch = SCREENM.out
| collect
MQCSCREENM(screen_out_ch, ch_mqc_conf, ch_mqc_logo)
}
if ( params.gbcov & bed != null ) {
GBCOV1M(bam_ch, chromo_sub)
.set { gbcov1 }
gbcov1_ch = GBCOV1M.out.sub_bam
//.concat(gbcov1.sub_bam_index)
.collect(flat : false)
// .map { it -> [it + it] }
//.view()
GBCOV2M(pin, bed_ch, gbcov1_ch)
}
if( params.genome != null ){
mqc_ch1 = STARM.out.read_per_gene_tab
.concat(STARM.out.log_final)
.collect()
//.view()
MQC(mqc_ch1, ch_mqc_conf, ch_mqc_logo)
COUNTSM(STARM.out.read_per_gene_tab.collect().flatten())
}
if( params.genome2 != null ){
STARM2(unmapped_ch, genome_ch2, splitName_ch )
mqc_ch2 = STARM2.out.read_per_gene_tab2
.concat(STARM2.out.log_final2)
.concat(mqc_ch1)
.collect()
//.view()
// mqc_ch3 = mqc_ch1.concat(mqc_ch2).view()
MQC2(mqc_ch2, ch_mqc_conf, ch_mqc_logo)
COUNTSM2(STARM2.out.read_per_gene_tab2.collect().flatten())
}
}
/* ---------------------------------------------------------------------------------------------------------
PAIRED END NOVA/NEXT-seq Workflow
------------------------------------------------------------------------------------------------------------ */
workflow PAIRED {
meta_ch = ch_sheet
| splitCsv( header:true )
| map { row -> [row.label, [file("fastqs/" + row.fastq1), file("fastqs/" + row.fastq2)]] }
| view
if(params.fastp){
FASTPM(meta_ch)
.set { fastp_out }
} else {
fastp_out = meta_ch
}
if (params.screen){
SCREENM(fastp_out, ch_screen_conf)
screen_out_ch = SCREENM.out
| collect
MQCSCREENM(screen_out_ch, ch_mqc_conf, ch_mqc_logo)
}
if( params.genome != null ){
STARM(fastp_out, genome_ch)
bam_ch = STARM.out.bam_sorted
| collect
| flatten
unmapped_ch = STARM.out.unmapped
// chromo_sub = channel.value(params.gbcov)
chromo_sub = channel.value(params.chromosub)
}
if ( params.gbcov & bed != null ) {
GBCOV1M(bam_ch, chromo_sub)
.set { gbcov1 }
gbcov1_ch = GBCOV1M.out.sub_bam
.collect(flat : false)
//.view()
GBCOV2M(pin, bed_ch, gbcov1_ch)
}
if( params.genome != null ){
mqc_ch1 = STARM.out.read_per_gene_tab
.concat(STARM.out.log_final)
.collect()
//.view()
MQC(mqc_ch1, ch_mqc_conf, ch_mqc_logo)
COUNTSM(STARM.out.read_per_gene_tab.collect().flatten())
}
if( params.genome2 != null ){
STARM2(unmapped_ch, genome_ch2, splitName_ch )
mqc_ch2 = STARM2.out.read_per_gene_tab2
.concat(STARM2.out.log_final2)
.concat(mqc_ch1)
.collect()
//.view()
// mqc_ch3 = mqc_ch1.concat(mqc_ch2).view()
MQC2(mqc_ch2, ch_mqc_conf, ch_mqc_logo)
COUNTSM2(STARM2.out.read_per_gene_tab2.collect().flatten())
}
}
workflow {
if ( params.mode == "SE" || params.mode == "SES" || params.mode == "SEBS" ){
SINGLE()
}
// else if ( params.mode == "UNMS" ){
// // SINGLE_SPLIT()
// }
else if ( params.mode == "PE" || params.mode == "PES" || params.mode == "PEBS" ){
PAIRED()
}
// else if ( params.mode == "UNMP" ){
// // PAIRED_SPLIT()
// }
else {
error "Invalid alignment mode provided"
exit 0
}
}
/* ---------------------------------------------------------------------------------------------------------
GLOBAL PROCESSES
------------------------------------------------------------------------------------------------------------ */