Initial addition #7089
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Initial addition #7089
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SPPearce
reviewed
Nov 26, 2024
| """ | ||
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| stub: | ||
| def args = task.ext.args ?: '' |
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Suggested change
| def args = task.ext.args ?: '' |
| } | ||
| } | ||
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| test("coptr extract single bam file") { |
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Is this one supposed to be a stub?
Suggested change
| test("coptr extract single bam file") { | |
| test("coptr extract single bam file - stub") { | |
| options "-stub" |
| 'biocontainers/coptr:1.1.4--pyhdfd78af_3' }" | ||
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| input: | ||
| tuple val(meta), path(bam, stageAs: "bamfolder/*") |
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Why are these being staged into the bamfolder, rather than just into the directory?
Can the tool not take . as the folder containing the bams?
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| coptr \ | ||
| extract \ | ||
| $args \ | ||
| bamfolder/ \ |
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| coptr \ | |
| extract \ | |
| $args \ | |
| bamfolder/ \ | |
| coptr \\ | |
| extract \\ | |
| $args \\ | |
| bamfolder/ \\ |
So the line breaks remain in the command executed
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PR checklist
Initial addition of module coptr/extract, fourth of five modules for the coptr package
Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
For modules:
- [X] nf-core modules test --profile docker
- [X] nf-core modules test --profile singularity
- [X] nf-core modules test --profile conda