Add stub block and migrate pairix to topic channels#11437
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HReed1 wants to merge 2 commits intonf-core:masterfrom
Open
Add stub block and migrate pairix to topic channels#11437HReed1 wants to merge 2 commits intonf-core:masterfrom
HReed1 wants to merge 2 commits intonf-core:masterfrom
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SPPearce
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Apr 30, 2026
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SPPearce
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Your version extraction is not working.
It does not need echo.
Please add a check step in your submission instructions that verifies the version is being extracted correctly
| [ | ||
| "PAIRIX", | ||
| "pairix", | ||
| "Program: pairix (PAIRs file InderXer)\n0.3.7\n\n\n\nOptions: -p STR preset: pairs, merged_nodups, old_merged_nodups, gff, bed, sam, vcf, psltbl [gff]\n -s INT sequence name column [1]\n -d INT second sequence name column [null]\n -b INT start1 column [4]\n -e INT end1 column; can be identical to '-b' [5]\n -u INT start2 column [null]\n -v INT end2 column; can be identical to '-u' [null or identical to the start2 specified by -u]\n -T delimiter is space instead of tab.\n -L query region is not a string but a file listing query regions\n -S INT skip first INT lines [0]\n -c CHAR symbol for comment/meta lines [#]\n -w CHAR symbol for query region separator [|]\n -r FILE replace the header with the content of FILE [null]\n -0 zero-based coordinate\n -h print also the header lines\n -H print only the header lines\n -B print only the number of bgzf blocks for existing chromosome (pairs)\n -W print only the region split character\n -Y Only check if the file is a triangle (i.e. a chromosome pair occurs only in one direction (e.g. if chr1|chr2 exists, chr2|chr1 doesn't))\n -l list chromosome names\n -n print only the total line count (same as gunzip -c | wc -l but much faster)\n -f force to overwrite the index\n -a autoflip query when the matching chromosome pair doesn't exist\n --help print usage with exit 0" |
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The version should be here instead.
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Changes
versions.ymlheredoc totopic: versionstuple patternstub:block with appropriate touch outputssnapshot(process.out).match()meta.ymlto align eval expressions withmain.nfVerification
nf-core modules lint pairix: 52/52 passed, 0 failuresnf-test(Docker): 2/2 passed, snapshots stable across consecutive runsPart of #4570