PROOF OF CONCEPT: samtools/multicommand#11550
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prototaxites wants to merge 6 commits intonf-core:masterfrom
Draft
PROOF OF CONCEPT: samtools/multicommand#11550prototaxites wants to merge 6 commits intonf-core:masterfrom
prototaxites wants to merge 6 commits intonf-core:masterfrom
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muffato
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May 7, 2026
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| def pipeline_command = pipeline.withIndex().collect { subcommand, idx -> | ||
| def argsKey = idx == 0 ? "args" : "args${idx + 1}" | ||
| def taskArgs = task.ext[argsKey] ?: "" | ||
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| def cmd_parts = ["samtools", subcommand] | ||
| if (taskArgs) { | ||
| cmd_parts << taskArgs | ||
| } | ||
| if (idx == 0) { | ||
| if (input_reference) { | ||
| cmd_parts << input_reference | ||
| } | ||
| cmd_parts << (input instanceof List ? input.join(" ") : input) | ||
| } | ||
| if (idx == n_commands - 1) { | ||
| if (output_reference) { | ||
| cmd_parts << output_reference | ||
| } | ||
| cmd_parts << output_string | ||
| } | ||
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| return cmd_parts.join(" ") | ||
| }.join(" |\\\n") |
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You just pipe the commands directly. Don't you need to add some - or -o - to force stdin/stdout ? I did that in my version https://github.com/nf-core/modules/pull/4571/changes#diff-34320bc32138ad0bc2d6a277f60183a5c4fc988b01314cab05ac6ff6245a9c94R38 , but perhaps that was unnecessary.
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AFAIK it's not mandatory in samtools?
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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.
Name TBD, and probably pending further discussion about the guidelines, how this fits and what would need to change.
PR checklist
Closes #XXX
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda