stubs and test for rnaseq modules - part V

[maxulysse]

Improve/fix stub, stub tests + single snapshot + snapshot versions:

• fastqc
• qualimap/bamqc
• qualimap/bamqccram
• qualimap/rnaseq
• picard/markduplicates
• samtools/flagstat
• samtools/idxstats
• samtools/index
• samtools/sort
• samtools/stats
• star/align
• star/genomegenerate
• stringtie/stringtie
• ucsc/bedgraphtobigwig

Updating snapshot for depending subworkflows:

• bam_dedup_stats_samtools_umitools
• bam_markduplicates_picard
• bam_sort_stats_samtools
• fastq_fastqc_umitools_fastp
• fastq_fastqc_umitools_trimgalore

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.
• Emit the versions.yml file.
• 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

[SPPearce]

This looks like it is just changes to the tests and a few more stub tests, no actual changes to the stub generation?

[maxulysse]

This looks like it is just changes to the tests and a few more stub tests, no actual changes to the stub generation?

Yes, I think I did update the actual stub generations in previous PRs

[maxulysse]

Hitting:

WARNING: Your kernel does not support CPU shares or the cgroup is not mounted. Shares discarded.
touch: .command.trace: Permission denied

Usually a relaunch does the trick, but I've retriggered enough time, and really want to merge this, so I'll be force merging this one.