Skip to content

Fix issues in chromograph module #9395

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

Merged
merged 11 commits into from
Nov 17, 2025
Merged

Fix issues in chromograph module #9395

Show file tree
Hide file tree
Changes from 7 commits
Commits
Show all changes
11 commits
Select commit Hold shift + click to select a range
0a8c6d8
Snapshot chromograph outputs
fellen31 Nov 12, 2025
fc5accb
Fix chromograph module
fellen31 Nov 12, 2025
4f6f001
format
fellen31 Nov 12, 2025
2ac9595
fix meta
fellen31 Nov 12, 2025
eacfe75
revert
fellen31 Nov 12, 2025
e445e4d
Add chrM to stub
fellen31 Nov 12, 2025
7517fd1
remove echo
fellen31 Nov 13, 2025
95767be
review comments
fellen31 Nov 14, 2025
0ea5564
Merge branch 'master' into chromograph-outputs
fellen31 Nov 14, 2025
be10a05
make reviewer happy inside
fellen31 Nov 17, 2025
937b4c6
Merge branch 'master' into chromograph-outputs
fellen31 Nov 17, 2025
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
98 changes: 41 additions & 57 deletions modules/nf-core/chromograph/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,12 @@
process CHROMOGRAPH {
tag "$meta.id"
// $meta.id can be [] because autozyg is not required, so use all ids
tag "${[meta, meta2, meta3, meta4, meta5, meta6, meta7].collect { meta_map -> meta_map.id }.findAll { id -> id }.join('_') ?: 'chromograph'}"
label 'process_single'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/chromograph:1.3.1--pyhdfd78af_2':
'biocontainers/chromograph:1.3.1--pyhdfd78af_2' }"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://depot.galaxyproject.org/singularity/chromograph:1.3.1--pyhdfd78af_2'
: 'biocontainers/chromograph:1.3.1--pyhdfd78af_2'}"

input:
tuple val(meta), path(autozyg)
Expand All @@ -17,79 +18,62 @@ process CHROMOGRAPH {
tuple val(meta7), path(sites)

output:
tuple val(meta), path("${prefix}"), emit: plots
path "versions.yml" , emit: versions
tuple val(meta), path("*.png"), emit: plots
path "versions.yml", emit: versions

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def autozyg_param = autozyg ? "--autozyg ${autozyg}" : ''
def coverage_param = coverage ? "--coverage ${coverage}" : ''
def exome_param = exome ? "--exom ${exome}" : ''
def fracsnp_param = fracsnp ? "--fracsnp ${fracsnp}" : ''
def ideogram_param = ideogram ? "--ideogram ${ideogram}" : ''
def regions_param = regions ? "--regions ${regions}" : ''
def sites_param = sites ? "--sites ${sites}" : ''
def args = task.ext.args ?: ''
def autozyg_param = autozyg ? "--autozyg ${autozyg}" : ''
def coverage_param = coverage ? "--coverage ${coverage}" : ''
def exome_param = exome ? "--exom ${exome}" : ''
def fracsnp_param = fracsnp ? "--fracsnp ${fracsnp}" : ''
def ideogram_param = ideogram ? "--ideogram ${ideogram}" : ''
def regions_param = regions ? "--regions ${regions}" : ''
def sites_param = sites ? "--sites ${sites}" : ''

if (autozyg) {
prefix = task.ext.prefix ?: "${meta.id}"
} else if (coverage) {
prefix = task.ext.prefix ?: "${meta2.id}"
} else if (exome) {
prefix = task.ext.prefix ?: "${meta3.id}"
} else if (fracsnp) {
prefix = task.ext.prefix ?: "${meta4.id}"
} else if (ideogram) {
prefix = task.ext.prefix ?: "${meta5.id}"
} else if (regions) {
prefix = task.ext.prefix ?: "${meta6.id}"
} else {
prefix = task.ext.prefix ?: "${meta7.id}"
}
"""
chromograph \\
$args \\
$autozyg_param \\
$coverage_param \\
$exome_param \\
$fracsnp_param \\
$ideogram_param \\
$regions_param \\
$sites_param \\
--outd ${prefix}
${args} \\
${autozyg_param} \\
${coverage_param} \\
${exome_param} \\
${fracsnp_param} \\
${ideogram_param} \\
${regions_param} \\
${sites_param} \\
--outd .

cat <<-END_VERSIONS > versions.yml
"${task.process}":
chromograph: \$(echo \$(chromograph --version 2>&1) | sed 's/chromograph //' )
chromograph: \$(chromograph --version | sed 's/.* //' )
END_VERSIONS
"""

stub:
def args = task.ext.args ?: ''
def args = task.ext.args ?: ''
euploidy = args.contains('-e') || args.contains('--euploid')

if (autozyg) {
prefix = task.ext.prefix ?: "${meta.id}"
} else if (coverage) {
prefix = task.ext.prefix ?: "${meta2.id}"
} else if (exome) {
prefix = task.ext.prefix ?: "${meta3.id}"
} else if (fracsnp) {
prefix = task.ext.prefix ?: "${meta4.id}"
} else if (ideogram) {
prefix = task.ext.prefix ?: "${meta5.id}"
} else if (regions) {
prefix = task.ext.prefix ?: "${meta6.id}"
} else {
prefix = task.ext.prefix ?: "${meta7.id}"
}
"""
mkdir ${prefix}
${touchCmd(euploidy, autozyg)}
${touchCmd(euploidy, coverage)}
${touchCmd(euploidy, exome)}
${touchCmd(euploidy, fracsnp)}
${touchCmd(euploidy, ideogram)}
${touchCmd(euploidy, regions)}
${touchCmd(euploidy, sites)}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
chromograph: \$(echo \$(chromograph --version 2>&1) | sed 's/chromograph //' )
chromograph: \$(chromograph --version | sed 's/.* //' )
END_VERSIONS
"""
}

// Helper function to generate touch commands
def touchCmd(euploidy, input_file) {
def chrs = euploidy ? (1..22) + ['X', 'Y', 'M'] : [1]
input_file ? chrs.collect { chr -> "touch ${input_file}_chr${chr}.png" }.join('\n') : ''
}
7 changes: 3 additions & 4 deletions modules/nf-core/chromograph/meta.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "chromograph"
description: Chromograph is a python package to create PNG images from genetics data
such as BED and WIG files.
Expand Down Expand Up @@ -88,10 +88,9 @@ output:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- ${prefix}:
- "*.png":
type: file
description: Directory containing the plots in png format
pattern: "*.png"
description: Plot(s) in PNG format
ontologies: []
versions:
- versions.yml:
Expand Down
143 changes: 131 additions & 12 deletions modules/nf-core/chromograph/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,33 +6,152 @@ nextflow_process {
tag "modules"
tag "modules_nfcore"
tag "chromograph"
config "./nextflow.config"

test("test_chromograph_sites") {
test("test_chromograph_sites_wig") {
when {
params {
module_args = ''
}
process {
"""
input[0] = [[],[]]
input[1] = Channel.of(
'fixedStep chrom=chr3 start=400601 step=100',
'11',
'22',
'33')
.collectFile(name: 'wig_input.wig', newLine: true)
.map { file -> [ [ id: file.name ], file ] }
input[2] = [[],[]]
input[3] = [[],[]]
input[4] = [[],[]]
input[5] = [[],[]]
input[6] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/updsites.bed', checkIfExists: true)
]
"""
}
}

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

test("test_chromograph_sites_wig_euploid") {
when {
params {
module_args = '--euploid'
}
process {
"""
input[0] = [[],[]]
input[1] = Channel.of(
'fixedStep chrom=chr3 start=400601 step=100',
'11',
'22',
'33')
.collectFile(name: 'wig_input.wig', newLine: true)
.map { file -> [ [ id: file.name ], file ] }
input[2] = [[],[]]
input[3] = [[],[]]
input[4] = [[],[]]
input[5] = [[],[]]
input[6] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/updsites.bed', checkIfExists: true)
]
"""
}
}

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

test("test_chromograph_sites_wig_stub") {

options "-stub"

when {
params {
module_args = ''
}
process {
"""
input[0] = [[:],[]]
input[1] = [[:],[]]
input[2] = [[:],[]]
input[3] = [[:],[]]
input[4] = [[:],[]]
input[5] = [[:],[]]
input[0] = [[],[]]
input[1] = Channel.of(
'fixedStep chrom=chr3 start=400601 step=100',
'11',
'22',
'33')
.collectFile(name: 'wig_input.wig', newLine: true)
.map { file -> [ [ id: file.name ], file ] }
input[2] = [[],[]]
input[3] = [[],[]]
input[4] = [[],[]]
input[5] = [[],[]]
input[6] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/updsites.bed', checkIfExists: true)
]
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/updsites.bed', checkIfExists: true)
]
"""
}
}

then {
assertAll(
{assert process.success},
{assert process.out.plots.get(0).get(1) ==~ ".*/test"}
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}

}

test("test_chromograph_sites_wig_euploid_stub") {

options "-stub"

when {
params {
module_args = '--euploid'
}
process {
"""
input[0] = [[],[]]
input[1] = Channel.of(
'fixedStep chrom=chr3 start=400601 step=100',
'11',
'22',
'33')
.collectFile(name: 'wig_input.wig', newLine: true)
.map { file -> [ [ id: file.name ], file ] }
input[2] = [[],[]]
input[3] = [[],[]]
input[4] = [[],[]]
input[5] = [[],[]]
input[6] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/updsites.bed', checkIfExists: true)
]
"""
}
}

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