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SPPearce
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Mar 3, 2026
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], // meta map | ||
| file('https://github.com/Plant-Food-Research-Open/assemblyqc/raw/eef371b57bda38fb0ff8167f7a547325c8211c3f/tests/hic/testdata/HYh1h2_Chr01_6000000_6015000.bam', checkIfExists: true), |
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We don't really like external data, is there not a suitable bam file in the test-datasets already?
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def VERSION = '20181227' | ||
| def args2 = task.ext.args2 ?: '' | ||
| def filter_cmd = args2 != '' ? "samtools view --threads $task.cpus $args2 -Sb $bam > ${prefix}.juicer.bam" : '' |
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Could this be piped into the other tool?
Should probably remove it afterwards anyway.
| bam2 \\ | ||
| juicer \\ | ||
| $juicer_input \\ | ||
| ${prefix}.links.txt |
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Can we not hardcode the .links here, put that into the default prefix instead.
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| matlock: $VERSION | ||
| samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') | ||
| END_VERSIONS |
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We have moved to using topic channels and eval for the versions, can you swap it please:
https://nf-co.re/hackathon-projects/hackathon-march-2026/modules
| e.g. `[ id:'sample1' ]` | ||
| - bam: | ||
| type: file | ||
| description: Sorted BAM/CRAM/SAM file |
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You'll need to stage the fasta as well for cram files (which samtools view could convert anyway if the tool didn't natively)
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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