Update parabricks minimap2 for scnanoseq#10788
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gburnett-nvidia wants to merge 7 commits intonf-core:masterfrom
Open
Update parabricks minimap2 for scnanoseq#10788gburnett-nvidia wants to merge 7 commits intonf-core:masterfrom
gburnett-nvidia wants to merge 7 commits intonf-core:masterfrom
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…es in old pipelines
SPPearce
reviewed
Mar 18, 2026
| tuple val(meta), path("*.cram"), emit: cram, optional: true | ||
| tuple val(meta), path("*.crai"), emit: crai, optional: true | ||
| tuple val(meta), path("*.{bam,cram}"), emit: bam, optional: true | ||
| tuple val(meta), path("*.{bai,crai}"), emit: index, optional: true |
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| tuple val(meta), path("*.{bai,crai}"), emit: index, optional: true | |
| tuple val(meta), path("*.{bai,csi,crai}"), emit: index, optional: true |
| description: index corresponding to sorted CRAM file | ||
| pattern: "*.crai" | ||
| description: Index corresponding to sorted BAM or CRAM file | ||
| pattern: "*.{bai,crai}" |
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| pattern: "*.{bai,crai}" | |
| pattern: "*.{bai,csi,crai}" |
| pattern: "*.crai" | ||
| description: Index corresponding to sorted BAM or CRAM file | ||
| pattern: "*.{bai,crai}" | ||
| ontologies: [] |
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This should have some ontologies, as should several of the others.
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| compatible_with: | ||
| \$(echo "\$pbrun_version_output" | tr '\\t' ' ' | awk -F':' '/Compatible With:/,/^---/ { if (\$0 !~ /Compatible With:/ && \$0 !~ /^---\$/ && index(\$0,":")>0) { key=\$1; val=\$2; gsub(/^[ ]+|[ ]+\$/, "", key); gsub(/^[ ]+|[ ]+\$/, "", val); printf " %s: %s\\n", key, val } }') |
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What is this really really long expression doing?
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This extracts the compatible version of the non-gpu tool so that you can directly see that in the snapshot. There is no reason to have this as a topic because this is specific for parabricks modules.
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| # We handle this different to the other modules because minimap does not begin with an Uppercase letter | ||
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| # Generate compatible_versions.yml | ||
| cat <<EOF > compatible_versions.yml |
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Can you swap to a topic channel please, which may make this unnecessary.
| ${args} | ||
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| # Capture the full version output once and store it in a variable | ||
| pbrun_version_output=\$(pbrun minimap2 --version 2>&1) |
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Why? Does the tool take a long time to give the version information?
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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