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Allow gzipped inputs to modkit/bedmethyltobigwig #9591

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Merged
fellen31 merged 3 commits into from
Dec 19, 2025
Merged

Allow gzipped inputs to modkit/bedmethyltobigwig #9591

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c68cd62
Allow gzipped inputs to modkit/bedmethyltobigwig
fellen31 Dec 19, 2025
f3bec60
Update modules/nf-core/modkit/bedmethyltobigwig/main.nf
fellen31 Dec 19, 2025
e586599
harshil
fellen31 Dec 19, 2025
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6 changes: 4 additions & 2 deletions modules/nf-core/modkit/bedmethyltobigwig/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -23,13 +23,15 @@ process MODKIT_BEDMETHYLTOBIGWIG {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def mods = modcodes instanceof List ? modcodes.join(',') : modcodes
input_cmd = bedmethyl.getName().endsWith('.gz') ? "gzip -cd" : "cat"
"""
modkit bedmethyl tobigwig \\
$input_cmd $bedmethyl |\\
modkit bedmethyl tobigwig \\
$args \\
--nthreads $task.cpus \\
--sizes $chromsizes \\
--mod-codes $mods \\
$bedmethyl \\
- \\
${prefix}.bw

cat <<-END_VERSIONS > versions.yml
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2 changes: 1 addition & 1 deletion modules/nf-core/modkit/bedmethyltobigwig/meta.yml
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Expand Up @@ -23,7 +23,7 @@ input:
- bedmethyl:
type: file
description: bedMethyl file
pattern: "*.{bed}"
pattern: "*.{bed,bed.gz}"
ontologies:
- edam: "http://edamontology.org/format_3003" # BED
- - meta2:
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4 changes: 2 additions & 2 deletions modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test
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Expand Up @@ -60,12 +60,12 @@ nextflow_process {
}
}

test("homo sapiens - bedmethyl, fai, string") {
test("homo sapiens - compressed bedmethyl, fai, string") {

when {
process {
"""
input[0] = TABIX_BGZIP.out.output
input[0] = MODKIT_PILEUP.out.bedgz
input[1] = [
[ id : 'hg38' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
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6 changes: 3 additions & 3 deletions modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap
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Expand Up @@ -65,7 +65,7 @@
},
"timestamp": "2025-12-11T14:17:52.811754475"
},
"homo sapiens - bedmethyl, fai, string": {
"homo sapiens - compressed bedmethyl, fai, string": {
"content": [
{
"0": [
Expand Down Expand Up @@ -94,8 +94,8 @@
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
"nextflow": "25.04.2"
},
"timestamp": "2025-12-11T14:18:02.079953932"
"timestamp": "2025-12-19T10:25:49.934420699"
}
}
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