diff --git a/software/gatk4/mergevcfs/meta.yml b/software/gatk4/mergevcfs/meta.yml index 05b4307b..5d6e053d 100644 --- a/software/gatk4/mergevcfs/meta.yml +++ b/software/gatk4/mergevcfs/meta.yml @@ -39,7 +39,7 @@ input: description: | Groovy Map containing sample information e.g. [ id:'test'] - - bam: + - vcf: type: list description: Two or more VCF files pattern: "*.{vcf,vcf.gz}" diff --git a/software/gatk4/revertsam/meta.yml b/software/gatk4/revertsam/meta.yml new file mode 100644 index 00000000..6d39d330 --- /dev/null +++ b/software/gatk4/revertsam/meta.yml @@ -0,0 +1,63 @@ +name: gatk4_revertsam +description: Reverts SAM or BAM files to a previous state. +keywords: + - sam + - revert +tools: + - gatk4: + description: | + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s + doi: 10.1158/1538-7445.AM2017-3590 +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$params.outdir/` + - publish_dir_mode: + type: string + description: | + Value for the Nextflow `publishDir` mode parameter. + Available: symlink, rellink, link, copy, copyNoFollow, move. + - enable_conda: + type: boolean + description: | + Run the module with Conda using the software specified + via the `conda` directive + - singularity_pull_docker_container: + type: boolean + description: | + Instead of directly downloading Singularity images for use with Singularity, + force the workflow to pull and convert Docker containers instead. +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - bam: + type: list + description: Two or more VCF files + pattern: "*.{vcf,vcf.gz}" + - ref_dict: + type: file + description: Optional Sequence Dictionary as input + pattern: "*.dict" + - use_ref_dict: + type: boolean + description: Specify whether or not to use a given reference dictionary +output: + - vcf: + type: file + description: merged vcf file + pattern: "*.vcf.gz" + - version: + type: file + description: File containing software version + pattern: "*.version.txt" +authors: + - "@kevinmenden" diff --git a/tests/software/gatk4/revertsam/main.nf b/tests/software/gatk4/revertsam/main.nf new file mode 100644 index 00000000..8d37f7ef --- /dev/null +++ b/tests/software/gatk4/revertsam/main.nf @@ -0,0 +1,18 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { GATK4_MERGEVCFS } from '../../../../software/gatk4/mergevcfs/main.nf' addParams( options: [:] ) + +workflow test_gatk4_mergevcfs { + + def input = [] + input = [ [ id:'test' ], // meta map + [ file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true), + file("${launchDir}/tests/data/vcf/test2.vcf.gz", checkIfExists: true), + file("${launchDir}/tests/data/vcf/test3.vcf.gz", checkIfExists: true) ] ] + + ref_dict = file("tests/data/fasta/test.consensus.for_vcf.dict", checkIfExists: true) + + GATK4_MERGEVCFS ( input, ref_dict, false ) +} diff --git a/tests/software/gatk4/revertsam/test.yml b/tests/software/gatk4/revertsam/test.yml new file mode 100644 index 00000000..c649e011 --- /dev/null +++ b/tests/software/gatk4/revertsam/test.yml @@ -0,0 +1,8 @@ +- name: gatk4 mergevcfs + command: nextflow run ./tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs -c tests/config/nextflow.config + tags: + - gatk4 + - gatk4_mergevcfs + files: + - path: output/gatk4/test.merged.vcf.gz + md5sum: f25850b7bd4d362b5ea67d4453e9df55