Fix issue #135: mutect2 fails with --no_intervals option

[lconde-ucl]

nf-core/sarek pull request

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Please fill in the appropriate checklist below (delete whatever is not relevant).
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PR checklist

• This pull request fixes errors in the HaplotypeCaller, GenotypeGVCFs, FreeBayes, Mutect2 and PileupSummariesForMutect2 processes when the pipeline is run with the '--no_intervals" option (it deletes the "-L no_intervals.bed" argument that was causing the problem). It also fixes a bug in the mpileupOut channel (it was generating all possible T-N combinations, similar to the issue Ascat computes all possible N-T combinations #136 in alleleCountOutput)
• If you've fixed a bug or added code that should be tested, add tests!
• If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: CONTRIBUTING.md

[maxulysse]

Can you add FreeBayes here to the list of tools?
https://github.com/lconde-ucl/sarek/blob/9af8391f28dc00dd7633c332bb9166b406cf44ee/.github/workflows/ci.yml#L103

[maxulysse]

LGTM