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main.nf
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#!/usr/bin/env nextflow
nextflow.enable.dsl=2
date = new Date().format( 'yyyyMMdd' )
log.info """\
L O G A N P I P E L I N E
=============================
genome: ${params.genome}
outdir: ${params.outdir}
Samples: ${params.fastq_input ?: ''} ${params.fastq_file_input ?: ''} ${params.bam_input ?: ''} ${params.bam_file_input ?: ''}
Sample Sheet: ${params.sample_sheet}
"""
.stripIndent()
include {DETERMINEBAM; INPUT; INPUT_BAM; ALIGN; GL;
VC; SV; CNVmouse; CNVhuman; CNVhuman_novc;
QC_GL; QC_NOGL; QC_GL_BAM; QC_NOGL_BAM} from "./subworkflows/local/workflows.nf"
include {INPUT_TONLY; INPUT_TONLY_BAM;
ALIGN_TONLY;
VC_TONLY; SV_TONLY; CNVmouse_tonly; CNVhuman_tonly; CNVhuman_novc_tonly;
QC_TONLY; QC_TONLY_BAM} from "./subworkflows/local/workflows_tonly.nf"
workflow.onComplete {
if (!workflow.stubRun && !workflow.commandLine.contains('-preview')) {
def message = Utils.spooker(workflow)
if (message) {
println message
}
}
}
//All Workflows
workflow {
//Tumor-Normal FASTQ
if ([params.fastq_input,params.fastq_file_input].any() && params.sample_sheet){
println "Tumor-Normal FASTQ"
INPUT()
ALIGN(INPUT.out.fastqinput,INPUT.out.sample_sheet)
//Germline
if (params.gl || params.germline){
GL(ALIGN.out.sample_sheet,ALIGN.out.bambyinterval)
}
//Tumor-Normal VC, SV, CNV
if (params.vc || params.snv){
VC(ALIGN.out.bamwithsample,ALIGN.out.splitout,ALIGN.out.sample_sheet)
}
if (params.sv || params.structural){
SV(ALIGN.out.bamwithsample)
}
if (params.cnv || params.copynumber){
if (params.genome.matches("mm10")){
CNVmouse(ALIGN.out.bamwithsample)
} else if (params.genome.matches("hg38(.*)") | params.genome.matches("hg19(.*)")){
if (!params.vc){
CNVhuman_novc(ALIGN.out.bamwithsample)
} else {
CNVhuman(ALIGN.out.bamwithsample,VC.out.somaticcall_input)
}
}
}
//QC Steps
if (params.qc && (params.gl || params.germline)){
QC_GL(ALIGN.out.fastqin,ALIGN.out.fastpout,ALIGN.out.bqsrout,
GL.out.glnexusout,GL.out.bcfout,ALIGN.out.fullinterval)
}else if (params.qc){
QC_NOGL(ALIGN.out.fastqin,ALIGN.out.fastpout,ALIGN.out.bqsrout,ALIGN.out.fullinterval)
}
}
//TUMOR-NORMAL BAM INPUT
if ([params.bam_input,params.bam_file_input].any() && params.sample_sheet){
println "Tumor-Normal BAM"
INPUT_BAM()
if (params.vc || params.snv ){
VC(INPUT_BAM.out.bamwithsample,INPUT_BAM.out.splitout,INPUT_BAM.out.sample_sheet)
}
if (params.sv || params.structural){
SV(INPUT_BAM.out.bamwithsample)
}
if (params.gl || params.germline){
GL(INPUT_BAM.out.sample_sheet,INPUT_BAM.out.bambyinterval)
}
if (params.cnv || params.copynumber){
if (params.genome.matches("mm10")){
CNVmouse(INPUT_BAM.out.bamwithsample)
} else if (params.genome.matches("hg38(.*)") | params.genome.matches("hg19(.*)")){
if (!(params.vc || params.snv)){
CNVhuman_novc(INPUT_BAM.out.bamwithsample)
}else {
CNVhuman(INPUT_BAM.out.bamwithsample,VC.out.somaticcall_input)
}
}
}
//QC Steps
if (params.qc && (params.gl || params.germline)){
QC_GL_BAM(INPUT_BAM.out.allbam,GL.out.glnexusout,GL.out.bcfout,INPUT_BAM.out.fullinterval)
}else if(params.qc){
QC_NOGL_BAM(INPUT_BAM.out.allbam,INPUT_BAM.out.fullinterval)
}
}
///Tumor Only Pipelines
if ([params.fastq_input,params.fastq_file_input].any() && !params.sample_sheet){
println "Tumor-Only FASTQ"
INPUT_TONLY()
ALIGN_TONLY(INPUT_TONLY.out.fastqinput,INPUT_TONLY.out.sample_sheet)
if (params.vc || params.snv){
VC_TONLY(ALIGN_TONLY.out.bamwithsample,ALIGN_TONLY.out.splitout,ALIGN_TONLY.out.sample_sheet)
}
if (params.sv || params.structural){
SV_TONLY(ALIGN_TONLY.out.bamwithsample)
}
if (params.cnv || params.copynumber){
if (params.genome.matches("mm10")){
CNVmouse_tonly(ALIGN_TONLY.out.bamwithsample)
} else if (params.genome.matches("hg38(.*)") | params.genome.matches("hg19(.*)")){
if (!(params.vc || params.snv)){
VC_TONLY(ALIGN_TONLY.out.bamwithsample,ALIGN_TONLY.out.splitout,ALIGN_TONLY.out.sample_sheet)
CNVhuman_tonly(ALIGN_TONLY.out.bamwithsample,VC_TONLY.out.somaticcall_input)
} else {
CNVhuman_tonly(ALIGN_TONLY.out.bamwithsample,VC_TONLY.out.somaticcall_input)
}
}
}
if (params.qc){
QC_TONLY(ALIGN_TONLY.out.fastqin,ALIGN_TONLY.out.fastpout,ALIGN_TONLY.out.bqsrout,ALIGN_TONLY.out.fullinterval)
}
}
//Variant Calling from BAM-Tumor Only Mode
if ([params.bam_input,params.bam_file_input].any() && !params.sample_sheet){
println "Tumor-Only BAM"
INPUT_TONLY_BAM()
if (params.vc || params.snv){
VC_TONLY(INPUT_TONLY_BAM.out.bamwithsample,INPUT_TONLY_BAM.out.splitout,INPUT_TONLY_BAM.out.sample_sheet)
}
if (params.sv || params.structural){
SV_TONLY(INPUT_TONLY_BAM.out.bamwithsample)
}
if (params.cnv || params.copynumber){
if (params.genome.matches("mm10")){
CNVmouse_tonly(INPUT_TONLY_BAM.out.bamwithsample)
}else if (params.genome.matches("hg38(.*)") | params.genome.matches("hg19(.*)")){
if (!(params.vc || params.snv)){
VC_TONLY(INPUT_TONLY_BAM.out.bamwithsample,INPUT_TONLY_BAM.out.splitout,INPUT_TONLY_BAM.out.sample_sheet)
CNVhuman_tonly(INPUT_TONLY_BAM.out.bamwithsample,VC_TONLY.out.somaticcall_input)
} else {
CNVhuman_tonly(INPUT_TONLY_BAM.out.bamwithsample,VC_TONLY.out.somaticcall_input)
}
}
}
if (params.qc){
QC_TONLY_BAM(INPUT_TONLY_BAM.out.bamwithsample,INPUT_TONLY_BAM.out.fullinterval)
}
}
}