main.nf

#!/usr/bin/env nextflow
nextflow.enable.dsl=2

// Import subworkflows to be run in the workflow
include { checkInputs       }   from './modules/check_cohort'
include { smoove            }   from './modules/smoove'
include { rehead_smoove     }   from './modules/smoove'
include { manta             }   from './modules/manta'
include { rehead_manta      }   from './modules/manta'
include { tiddit_sv         }   from './modules/tiddit_sv'
include { rehead_tiddit     }   from './modules/tiddit_sv'
include { tiddit_cov        }   from './modules/tiddit_cov'
include { survivor_merge    }   from './modules/survivor_merge'
include { survivor_summary  }   from './modules/survivor_summary'
include { annotsv           }   from './modules/annotsv'

// Print the header to screen when running the pipeline
log.info """\

===================================================================
G E R M L I N E  S T R U C T U R A L  V - N F
===================================================================

Created by the Sydney Informatics Hub, University of Sydney

Documentation	@ https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf

Cite					@ 10.48546/workflowhub.workflow.431.1

Log issues		@ https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/issues

===================================================================
Workflow run parameters
===================================================================

 version          : ${params.version}
 input            : ${params.input}
 reference        : ${params.ref}
 manta intervals  : ${params.intervals}
 max merge dist   : ${params.survivorMaxDist}
 caller consensus : ${params.survivorConsensus}
 type agreement   : ${params.survivorType}
 strand agreement : ${params.survivorStrand}
 minMerge size    : ${params.survivorSize}
 annotsvDir       : ${params.annotsvDir}
 genomeBuild      : ${params.genomeBuild}
 annotsvMode      : ${params.annotsvMode}
 outDir           : ${params.outDir}
 workDir          : ${workflow.workDir}

===================================================================
Extra flags
===================================================================

 manta flags      : ${params.extraMantaFlags}
 smoove flags     : ${params.extraSmooveFlags}
 tiddit cov flags : ${params.extraTidditCovFlags}
 tiddit SV flags  : ${params.extraTidditSvFlags}
 annotSV flags    : ${params.extraAnnotsvFlags}

===================================================================
 """

// Help function
// FYI: formatting below looks messy in vs code file viewer but lines up nicely in terminal
def helpMessage() {
log.info"""

Usage:  nextflow run main.nf --input samplesheet.tsv --ref reference.fasta

Required Arguments:

	--input			    Full path and name of sample input file (tsv format).

	--ref			    Full path and name of reference genome (fasta format).

Optional Arguments:

	--outDir		    Full path and name of results directory.

	--intervals		    Full path and name of the intervals file for Manta (bed format).

	--survivorMaxDist           Maximum distance between SVs to merge (default: 1000bp).

	--survivorConsensus         Number of supportive callers require to report event (default: 1).

	--survivorType		    Callers must agree on event type before merging calls (default: yes[1]).

	--survivorStrand	    Callers must identify event on same strand before merging calls (default: yes[1]).

	--survivorSize		    Minimum size (bp) event to report (default 40bp).

	--annotsvDir		    Full path to the directory housing the prepared AnnotSV directory.
	
	--genomeBuild		    Genome version from annotsvDir downloaded files (default: GRCh37).

	--annotsvMode		    Specify full, split, or both for AnnotSV output mode (default: both).

	--extraMantaFlags	    Additionally specify any valid Manta flags.

	--extraSmooveFlags	    Additionally specify any valid Smoove flags.

	--extraTidditSvFlags        Additionally specify any valid Tiddit SV flags.

	--extraTidditCovFlags       Additionally specify any valid Tiddit Cov flags.

	--extraAnnotsvFlags         Additionally specify any valid AnnotSV flags.

HPC accounting arguments:

        --whoami                    HPC user name (Setonix or Gadi HPC)

        --gadi_account              Project accounting code for NCI Gadi (e.g. aa00)

        --setonix_account           Project accounting code for Pawsey Setonix (e.g. name1234)
""".stripIndent()
}

workflow {

if ( params.help == true || params.ref == false || params.input == false ){
	// Invoke the help function above and exit
	helpMessage()
	exit 1

	} else {

	// Check inputs file exists
	checkInputs(Channel.fromPath(params.input, checkIfExists: true))

	// Split cohort file to collect info for each sample
	input = checkInputs.out
		.splitCsv(header: true, sep:"\t")
		.map { row -> tuple(row.sampleID, file(row.bam), file(row.bai))}

	// Call SVs with Manta
	manta(input, params.ref, params.ref+'.fai')

	// Rehead manta vcf for merging
	rehead_manta(manta.out.manta_diploid_convert, manta.out.manta_diploid_convert_tbi)

	// Call SVs with Smoove
	smoove(input, params.ref, params.ref+'.fai')

	// Rehead smoove vcf for merging
	rehead_smoove(smoove.out.smoove_geno)

	// Run TIDDIT sv
	tiddit_sv(input, params.ref, params.ref+'.fai')

	// Rehead TIDDIT vcf for merging
	rehead_tiddit(tiddit_sv.out.tiddit_vcf)

	// Run TIDDIT cov
	tiddit_cov(input, params.ref, params.ref+'.fai')

	// Collect VCFs for merging
	mergeFile = rehead_tiddit.out.tiddit_VCF
		.concat(rehead_smoove.out.smoove_VCF, rehead_manta.out.manta_VCF)
		.groupTuple()

	// Run SURVIVOR merge
	survivor_merge(mergeFile)

	// Run SURVIVOR summary
	survivor_summary(survivor_merge.out.mergedVCF)

	// Run AnnotSV (optional)
	if (params.annotsvDir) {
		annotsv(survivor_merge.out.mergedVCF, params.annotsvDir, params.annotsvMode)}
	}}

workflow.onComplete {

summary = """
===================================================================
Workflow execution summary
===================================================================

Duration		: ${workflow.duration}
Success			: ${workflow.success}
workDir			: ${workflow.workDir}
Exit status	: ${workflow.exitStatus}
outDir			: ${params.outDir}

===================================================================

"""

println summary

}