Using GATKs mergeVcfs

[asp8200]

Closes #569

Using GATK4's module mergeVcfs instead of modules/local/concat_vcf/main.nf + bin/concatenateVCFs.sh.

With this PR, the nf-core-module with GATK4's mergeVcfs is now being included in Sarek.

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[maxulysse]

<3

[maxulysse]

some failures in the CI.
I don't care much about gatk4_spark and mutect2 as I know they're difficult, but concerned about haplotypecaller and variantcalling_channel

[FriederikeHanssen]

Great work. Just update the changelog and two indents and then ready to merge 🚀

Edit: Didn't see the failing variantcaller test. Let me see if I can find a reason quickly

[asp8200]

some failures in the CI. I don't care much about gatk4_spark and mutect2 as I know they're difficult, but concerned about haplotypecaller and variantcalling_channel

@FriederikeHanssen confirmed that there is no problem with the variantcalling_channel. It was apparently just a glitch in the execution of the CI-tests on GitHub. (There seems to be a lot of such glitches with the CI-tests recently.)

The problem with the haplotypecaller-test is that the test expects an output-vcf-file called sample1.vcf.gz but the hyplotypecaller produces a vcf-file called sample1.g.vcf.gz. The problem is also on the dev-branch (6cf0b12). The docs/output.md seem to indicate that the output-vcf-files should be named in another way:

sarek/docs/output.md

Lines 229 to 232 in c60ef1f

	**Output directory: `results/VariantCalling/[SAMPLE]/HaplotypeCallerGVCF`**
	- `HaplotypeCaller_[SAMPLE].g.vcf.gz` and `HaplotypeCaller_[SAMPLE].g.vcf.gz.tbi`
	- `VCF` with Tabix index

[maxulysse]

@nf-core-bot fix linting please

[FriederikeHanssen]

Yeah don't worry about haplotypecaller, the PR is already open to fix that subworkflow, just need to finish it. I will fix the CI there