Samtools quickcheck

[Krannich479]

PR checklist

Closes #9657

• This comment contains a description of changes (with reason).
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Summary

This PR adds samtools quickcheck to the nf-core modules. As opposed to many other tools, this samtools submodule does not return an output file. Instead, the command returns a non-zero exit code if the alignment file (SAM/BAM/CRAM) is invalid/malformatted.
The nf-core module specification does not strictly require output files. The idea here is to use the exit code of samtools for it's native behavior, i.e. the exit code determines the success of the nextflow workflow (regulated by the errorStrategy). If the input channel contains an invalid alignment file, the nf-core module returns a non-zero exit code and terminates the main worflow.

[prototaxites]

A thought about how this might be made more malleable to pipeline developers.

I wonder if linting is failing because the module has no "ordinary" outputs?

[prototaxites]

Suggested change

// TODO nf-core: Once you have added the required tests, please run the following command to build this file:

[prototaxites]

Suggestion: instead of erroring the process, we should capture the exitcode in the script and then return it.

This allows more flexibility to the module user - they can iterate over the outputs of the module and either filter out failed BAM files, throw an error, try and fix problems, etc.. - rather than just forcing the pipeline to die.

Suggested change

	/* There is not generated output files.
	The sole purpose of 'samtools quickcheck' is to return an error if the mapping file is malformatted.
	The purpose in of the Nextflow process is to break the main workflow (by default) if the script returns a non-zero exit code.
	The nf-core components guidelines (https://nf-co.re/docs/guidelines/components/modules) do not specify that there must be output files.
	*/
	tuple val(meta), path(bam), env("EXIT_CODE")

[prototaxites]

Suggested change

	samtools quickcheck \\
	$args \\
	$bam
	samtools quickcheck \\
	$args \\
	$bam || EXIT_CODE=\$?
	EXIT_CODE=\${EXIT_CODE:-0}

[prototaxites]

Suggested change

	echo $args
	EXIT_CODE=0
	echo $args