From efd60d94eecd3670e588d678e467691d1185b6c4 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Mon, 22 Feb 2021 15:10:20 +0100
Subject: [PATCH] adding revertsam/ fix typo in mergevcfs

---
 software/gatk4/mergevcfs/meta.yml       |  2 +-
 software/gatk4/revertsam/meta.yml       | 63 +++++++++++++++++++++++++
 tests/software/gatk4/revertsam/main.nf  | 18 +++++++
 tests/software/gatk4/revertsam/test.yml |  8 ++++
 4 files changed, 90 insertions(+), 1 deletion(-)
 create mode 100644 software/gatk4/revertsam/meta.yml
 create mode 100644 tests/software/gatk4/revertsam/main.nf
 create mode 100644 tests/software/gatk4/revertsam/test.yml

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 `$params.outdir/<SOFTWARE>`
+  - publish_dir_mode:
+      type: string
+      description: |
+        Value for the Nextflow `publishDir` mode parameter.
+        Available: symlink, rellink, link, copy, copyNoFollow, move.
+  - enable_conda:
+      type: boolean
+      description: |
+        Run the module with Conda using the software specified
+        via the `conda` directive
+  - singularity_pull_docker_container:
+      type: boolean
+      description: |
+        Instead of directly downloading Singularity images for use with Singularity,
+        force the workflow to pull and convert Docker containers instead.
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - bam:
+      type: list
+      description: Two or more VCF files
+      pattern: "*.{vcf,vcf.gz}"
+  - ref_dict:
+      type: file
+      description: Optional Sequence Dictionary as input
+      pattern: "*.dict"
+  - use_ref_dict:
+      type: boolean
+      description: Specify whether or not to use a given reference dictionary
+output:
+  - vcf:
+      type: file
+      description: merged vcf file
+      pattern: "*.vcf.gz"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.version.txt"
+authors:
+  - "@kevinmenden"
diff --git a/tests/software/gatk4/revertsam/main.nf b/tests/software/gatk4/revertsam/main.nf
new file mode 100644
index 00000000..8d37f7ef
--- /dev/null
+++ b/tests/software/gatk4/revertsam/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_MERGEVCFS } from '../../../../software/gatk4/mergevcfs/main.nf' addParams( options: [:] )
+
+workflow test_gatk4_mergevcfs {
+
+    def input = []
+    input = [ [ id:'test' ], // meta map
+              [ file("${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