Skip to content

Add stub block and migrate pairix to topic channels #11437

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
HReed1 wants to merge 2 commits into
base: master
Choose a base branch
from
+112 −20
Open

Add stub block and migrate pairix to topic channels #11437

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
7351e3b
feat(pairix): migrate to topic versions and stub
HReed1 Apr 30, 2026
8048159
fix(pairix): align meta.yml with main.nf and simplify snapshot assert…
HReed1 Apr 30, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 7 additions & 5 deletions modules/nf-core/pairix/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ process PAIRIX {

output:
tuple val(meta), path(pair), path("*.px2"), emit: index
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('pairix'), eval('echo "$(pairix --help 2>&1)" | sed "s/^.*Version: //; s/Usage.*$//"'), topic: versions, emit: versions_pairix

when:
task.ext.when == null || task.ext.when
Expand All @@ -23,10 +23,12 @@ process PAIRIX {
pairix \\
$args \\
$pair
"""

cat <<-END_VERSIONS > versions.yml
"${task.process}":
pairix: \$(echo \$(pairix --help 2>&1) | sed 's/^.*Version: //; s/Usage.*\$//')
END_VERSIONS
stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${pair}.px2
"""
}
32 changes: 24 additions & 8 deletions modules/nf-core/pairix/meta.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,11 +8,13 @@ keywords:
- pairs
tools:
- pairix:
description: 2D indexing on bgzipped text files of paired genomic coordinates
description: 2D indexing on bgzipped text files of paired genomic
coordinates
homepage: "https://github.com/4dn-dcic/pairix"
documentation: "https://github.com/4dn-dcic/pairix"
tool_dev_url: "https://github.com/4dn-dcic/pairix"
licence: ["MIT"]
licence:
- "MIT"
identifier: biotools:pairix
input:
- - meta:
Expand Down Expand Up @@ -41,13 +43,27 @@ output:
description: pair index file
pattern: "*.px2"
ontologies: []
versions_pairix:
- - ${task.process}:
type: string
description: The name of the process
- pairix:
type: string
description: The name of the tool
- 'echo "$(pairix --help 2>&1)" | sed "s/^.*Version: //; s/Usage.*$//"':
type: eval
description: The expression to obtain the version of the tool
topics:
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
- - ${task.process}:
type: string
description: The name of the process
- pairix:
type: string
description: The name of the tool
- 'echo "$(pairix --help 2>&1)" | sed "s/^.*Version: //; s/Usage.*$//"':
type: eval
description: The expression to obtain the version of the tool
authors:
- "@jianhong"
maintainers:
Expand Down
21 changes: 21 additions & 0 deletions modules/nf-core/pairix/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,4 +29,25 @@ nextflow_process {
}
}

test("test-pairix-stub") {
options "-stub"

when {
process {
"""
input[0] = [ [ id:'test', single_end:false ], // meta map
file("https://raw.githubusercontent.com/4dn-dcic/pairix/master/samples/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz", checkIfExists: true) ]

"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}

}
67 changes: 60 additions & 7 deletions modules/nf-core/pairix/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,11 @@
]
],
"1": [
"versions.yml:md5,848c8be602ec36645d30010ea30f0684"
[
"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"
Copy link
Copy Markdown
Member

@mribeirodantas mribeirodantas Apr 30, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The version should be here instead.

]
],
"index": [
[
Expand All @@ -25,15 +29,64 @@
"4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2:md5,a6e41cc7cff16fd15b5ee505549ec99a"
]
],
"versions": [
"versions.yml:md5,848c8be602ec36645d30010ea30f0684"
"versions_pairix": [
[
"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"
]
]
}
],
"timestamp": "2026-04-30T12:47:18.779231",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
},
"test-pairix-stub": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"4dn.bsorted.chr21_22_only.nontriangle.pairs.gz:md5,ee90dc99987ece492d598ed939d54561",
"4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
[
"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"
]
],
"index": [
[
{
"id": "test",
"single_end": false
},
"4dn.bsorted.chr21_22_only.nontriangle.pairs.gz:md5,ee90dc99987ece492d598ed939d54561",
"4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions_pairix": [
[
"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"
]
]
}
],
"timestamp": "2026-04-30T12:47:22.756575",
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-23T11:25:18.874503"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
}
}
Loading