Verified Commit e363dd6f authored by Laurent Modolo's avatar Laurent Modolo
Browse files

add example of variant calling with gatk4

parent 6f67c65c
nextflow.enable.dsl=2
/*
Testing pipeline for marseq scRNASeq analysis
*/
include {
mapping;
} from "./nf_modules/bwa/main.nf"
include {
mapping;
} from "./nf_modules/gatk4/main.nf" addParams(
variant_calling_out: "vcf/",
)
channel
.fromFilePairs( params.fastq, size: -1)
.set { fastq_files }
channel
.fromPath( params.fasta )
.ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
.map { it -> [it.simpleName, it]}
.set { fasta_files }
workflow {
mapping(fasta, fastq_files)
germline_cohort_data_variant_calling(mapping.out.bam, fasta)
}
......@@ -10,6 +10,7 @@ include {
mark_duplicate;
} from './nf_modules/picard/main.nf'
params.variant_calling_out = ""
workflow germline_cohort_data_variant_calling {
take:
bam
......@@ -234,6 +235,9 @@ process genomic_db_call {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
if (params.variant_calling_out != "") {
publishDir "results/${params.variant_calling_out}", mode: 'copy'
}
input:
tuple val(file_id), path(db)
tuple val(ref_id), path(fasta), path(fai), path(dict)
......
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