PROOF OF CONCEPT: samtools/multicommand

[prototaxites]

See discussion on the nf-core slack: https://nfcore.slack.com/archives/C043UU89KKQ/p1777986494144269

Here is a working example of a "samtools/multicommand" module that constructs a chain of samtools commands that pipe into each other following a user-specified input describing which tools to use.

Currently the supported commands are only those which write *AM or fasta/fastq - I think that limits the scope helpfully. If you want to run samtools stats, for example, pass the output from this into that dedicated module.

# valid commands:
['view', 'sort', 'markdup', 'fixmate', 'merge', 'cat', 'collate', 'fastq', 'fasta']

The exact order of operations is specified by the pipeline input, which takes a list such as [view, sort, markdup]. This is then interpolated to a script where the output of each command is streamed to the next before being written to disk. The script can handle references being passed, as well as writing indexes, outputting in CRAM format, and conversion to FASTA and FASTQ.

By default, the threads for each tool are set to the total number of available cpus. However, it may be desirable to configure the number of threads used for each step, for example to give more threads to samtools sort than to samtools view. This can be achieved by specifying a number of threads in $argsX with -@, which will override the number of threads for that command. There is no sanity check that the number of threads is less than the total number available when doing this.

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

[muffato]

Good for me !

[prototaxites]

I will see if anyone else wants to weigh in before I merge!