Pytest -> Nftest Readwriter

[FriederikeHanssen]

PR contains two changes:

• Migrate SENTIEON_READWRITER module test from pytest to nftest
• Allows to input bam and output cram files by using prefix similarly to other modules that convert data. This also enables a wider range of conversions: bam -> merge -> cram

[FriederikeHanssen]

[adamrtalbot]

N E X T F L O W  ~  version 24.04.3
  Launching `/home/ubuntu/tests/383906a652037bde7b4222e478bc2ff/meta/mock.nf` [pensive_hodgkin] DSL2 - revision: 3fd844ab48
  WARN: Input tuple does not match tuple declaration in process `SENTIEON_READWRITER` -- offending value: [[id:test], [/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam, /nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam, /nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam], [/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai, /nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai, /nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai], []]

[FriederikeHanssen]

N E X T F L O W  ~  version 24.04.3
  Launching `/home/ubuntu/tests/383906a652037bde7b4222e478bc2ff/meta/mock.nf` [pensive_hodgkin] DSL2 - revision: 3fd844ab48
  WARN: Input tuple does not match tuple declaration in process `SENTIEON_READWRITER` -- offending value: [[id:test], [/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam, /nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam, /nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam], [/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai, /nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai, /nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai], []]

🤦‍♀️ good catch