From e363dd6fcbb5445a41d9cb9d32693f99a0f4e751 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 2 Jun 2021 10:54:50 +0200
Subject: [PATCH] add example of variant calling with gatk4
---
src/example_variant_calling.nf | 29 +++++++++++++++++++++++++++++
src/nf_modules/gatk4/main.nf | 4 ++++
2 files changed, 33 insertions(+)
create mode 100644 src/example_variant_calling.nf
diff --git a/src/example_variant_calling.nf b/src/example_variant_calling.nf
new file mode 100644
index 00000000..963cde03
--- /dev/null
+++ b/src/example_variant_calling.nf
@@ -0,0 +1,29 @@
+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: ${params.fasta}" }
+ .map { it -> [it.simpleName, it]}
+ .set { fasta_files }
+
+workflow {
+ mapping(fasta, fastq_files)
+ germline_cohort_data_variant_calling(mapping.out.bam, fasta)
+}
diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf
index 2f23b9e2..bb072eb6 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -10,6 +10,7 @@ include {
mark_duplicate;
} from './nf_modules/picard/main.nf'
+params.variant_calling_out = ""
workflow germline_cohort_data_variant_calling {
take:
bam
@@ -234,6 +235,9 @@ process genomic_db_call {
container = "${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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