Convert remaining pytests to nf-test

[famosab]

I thought having an overview issue to keep track of converting the pipeline level tests to nf-test would be practical. This is the list of the pytest yml files (some of them can maybe be combined? / some of them might already be ported but the pytest still has to be deleted?):

• [x] https://github.com/nf-core/sarek/pull/1825
• [x] https://github.com/nf-core/sarek/pull/1866
• [x] https://github.com/nf-core/sarek/pull/1831
• [x] https://github.com/nf-core/sarek/pull/1821
• [x] https://github.com/nf-core/sarek/pull/1867
• [x] haplotypecaller_skip_filter - https://github.com/nf-core/sarek/pull/1827
• [x] haplotypecaller - https://github.com/nf-core/sarek/pull/1827
• [x] https://github.com/nf-core/sarek/pull/1868
• [x] joint_germline - https://github.com/nf-core/sarek/pull/1874
• [x] https://github.com/nf-core/sarek/pull/1828
• [x] https://github.com/nf-core/sarek/pull/1820
• [x] https://github.com/nf-core/sarek/pull/1826
• [x] msisensorpro - https://github.com/nf-core/sarek/pull/1877
• [x] mutect2 - https://github.com/nf-core/sarek/pull/1874
• [x] ngscheckmate - https://github.com/nf-core/sarek/pull/1876
• [x] save_output_as_bam_only - https://github.com/nf-core/sarek/pull/1678
• [ ] sentieon_aligner_bwamem
• [ ] sentieon_dedup_from_bam
• [ ] sentieon_dnascope_skip_filter
• [ ] sentieon_dnascope_joint_germline
• [ ] sentieon_dnascope
• [ ] sentieon_haplotyper_joint_germline
• [ ] sentieon_haplotyper_skip_filter
• [ ] sentieon_haplotyper
• [x] https://github.com/nf-core/sarek/pull/1819
• [ ] tools_manually - part in https://github.com/nf-core/sarek/pull/1974
• [x] umi - https://github.com/nf-core/sarek/pull/1878

[maxulysse]

I'm on tiddit and manta

[SPPearce]

I made nf-tests for ngscheckmate in the modules repo if it helps