porting subworkflow Bam applybqsr to nf core modules

[agrima2010]

PR checklist

Closes #XXX

• 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 - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Broadcast software version numbers to topic: versions - See version_topics
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[maxulysse]

Suggested change

	include { SAMTOOLS_MERGE as MERGE_BAM } from '../../../modules/nf-core/samtools/merge/main'
	include { SAMTOOLS_MERGE as MERGE_CRAM } from '../../../modules/nf-core/samtools/merge/main'
	include { SAMTOOLS_MERGE as MERGE_BAM } from '../../../modules/nf-core/samtools/merge'
	include { SAMTOOLS_MERGE as MERGE_CRAM } from '../../../modules/nf-core/samtools/merge'

[maxulysse]

Suggested change

	bam // channel: [mandatory] [ meta, bam, bai, recal ]
	cram // channel: [mandatory] [ meta, cram, crai, recal ]
	reads // channel: [mandatory] [ meta, reads, index, recal ]
	``