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Merged
jkh00 merged 3 commits into from
Apr 7, 2025
Merged

Update modkit and porechop modules #8223

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3dfefa2
Update modkit and porechop modules
Apr 7, 2025
ddcaca2
update link to porechop singularity container
Apr 7, 2025
fd2bb52
update link
Apr 7, 2025
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2 changes: 1 addition & 1 deletion modules/nf-core/modkit/pileup/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- ont-modkit=0.3.0
- ont-modkit=0.4.3
6 changes: 3 additions & 3 deletions modules/nf-core/modkit/pileup/main.nf
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Expand Up @@ -4,12 +4,12 @@ process MODKIT_PILEUP {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ont-modkit:0.3.0--h5c23e0d_0':
'biocontainers/ont-modkit:0.3.0--h5c23e0d_0' }"
'https://depot.galaxyproject.org/singularity/ont-modkit:0.4.3--hcdda2d0_0':
'biocontainers/ont-modkit:0.4.3--hcdda2d0_0' }"

input:
tuple val(meta), path(bam), path(bai)
tuple val(meta2), path(fasta)
tuple val(meta2), path(fasta), path(fai)
tuple val(meta3), path(bed)

output:
Expand Down
4 changes: 4 additions & 0 deletions modules/nf-core/modkit/pileup/meta.yml
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Expand Up @@ -37,6 +37,10 @@ input:
description: Reference sequence in FASTA format. Required for motif (e.g. CpG)
filtering
pattern: "*.fasta"
- fai:
type: file
description: Associated index file for FASTA
pattern: "*.fai"
- - meta3:
type: map
description: |
Expand Down
54 changes: 32 additions & 22 deletions modules/nf-core/modkit/pileup/tests/main.nf.test
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Expand Up @@ -18,7 +18,7 @@ nextflow_process {
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam.bai', checkIfExists: true)
]
input[1] = [[],[]]
input[1] = [[],[],[]]
input[2] = [[],[]]
"""
}
Expand All @@ -33,7 +33,7 @@ nextflow_process {

}

test("[bam, bai], fasta, []") {
test("[bam, bai], [fasta, fai], []") {

when {
process {
Expand All @@ -45,7 +45,8 @@ nextflow_process {
]
input[1] = [
[ id: 'test_ref' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
]
input[2] = [[],[]]
"""
Expand All @@ -61,7 +62,7 @@ nextflow_process {

}

test("[bam, bai], fasta, bed") {
test("[bam, bai], [fasta, fai], bed") {

when {
process {
Expand All @@ -73,7 +74,8 @@ nextflow_process {
]
input[1] = [
[ id: 'test_ref' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
]
input[2] = Channel.of('chr22\t0\t1000')
.collectFile(name: 'chr22.bed', newLine: true)
Expand All @@ -91,7 +93,7 @@ nextflow_process {

}

test("[bam, bai], fasta, bed - traditional") {
test("[bam, bai], [fasta, fai], bed - traditional") {

config "./nextflow.traditional.config"

Expand All @@ -105,7 +107,8 @@ nextflow_process {
]
input[1] = [
[ id: 'test_ref' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
]
input[2] = Channel.of('chr22\t0\t1000')
.collectFile(name: 'chr22.bed', newLine: true)
Expand All @@ -123,7 +126,7 @@ nextflow_process {

}

test("[bam, bai], fasta, bed - traditional, HP") {
test("[bam, bai], [fasta, fai], bed - traditional, HP") {

config "./nextflow.traditional_hp.config"

Expand All @@ -137,7 +140,8 @@ nextflow_process {
]
input[1] = [
[ id: 'test_ref' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
]
input[2] = Channel.of('chr22\t0\t1000')
.collectFile(name: 'chr22.bed', newLine: true)
Expand All @@ -155,7 +159,7 @@ nextflow_process {

}

test("[bam, bai], fasta, bed - traditional, HP, bedgraph") {
test("[bam, bai], [fasta, fai], bed - traditional, HP, bedgraph") {

config "./nextflow.traditional_hp_bedgraph.config"

Expand All @@ -169,7 +173,8 @@ nextflow_process {
]
input[1] = [
[ id: 'test_ref' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
]
input[2] = Channel.of('chr22\t0\t1000')
.collectFile(name: 'chr22.bed', newLine: true)
Expand Down Expand Up @@ -199,7 +204,7 @@ nextflow_process {
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam.bai', checkIfExists: true)
]
input[1] = [[],[]]
input[1] = [[],[],[]]
input[2] = [[],[]]
"""
}
Expand All @@ -214,7 +219,7 @@ nextflow_process {

}

test("[bam, bai], fasta, [] - stub") {
test("[bam, bai], [fasta, fai], [] - stub") {

options "-stub"

Expand All @@ -228,7 +233,8 @@ nextflow_process {
]
input[1] = [
[ id: 'test_ref' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
]
input[2] = [[],[]]
"""
Expand All @@ -244,7 +250,7 @@ nextflow_process {

}

test("[bam, bai], fasta, bed - stub") {
test("[bam, bai], [fasta, fai], bed - stub") {

options "-stub"

Expand All @@ -258,7 +264,8 @@ nextflow_process {
]
input[1] = [
[ id: 'test_ref' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
]
input[2] = Channel.of('chr22\t0\t1000')
.collectFile(name: 'chr22.bed', newLine: true)
Expand All @@ -276,7 +283,7 @@ nextflow_process {

}

test("[bam, bai], fasta, bed - traditional - stub") {
test("[bam, bai], [fasta, fai], bed - traditional - stub") {

config "./nextflow.traditional.config"
options "-stub"
Expand All @@ -291,7 +298,8 @@ nextflow_process {
]
input[1] = [
[ id: 'test_ref' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
]
input[2] = Channel.of('chr22\t0\t1000')
.collectFile(name: 'chr22.bed', newLine: true)
Expand All @@ -309,7 +317,7 @@ nextflow_process {

}

test("[bam, bai], fasta, bed - traditional, HP - stub") {
test("[bam, bai], [fasta, fai], bed - traditional, HP - stub") {

config "./nextflow.traditional_hp.config"
options "-stub"
Expand All @@ -324,7 +332,8 @@ nextflow_process {
]
input[1] = [
[ id: 'test_ref' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
]
input[2] = Channel.of('chr22\t0\t1000')
.collectFile(name: 'chr22.bed', newLine: true)
Expand All @@ -342,7 +351,7 @@ nextflow_process {

}

test("[bam, bai], fasta, bed - traditional, HP, bedgraph - stub") {
test("[bam, bai], [fasta, fai], bed - traditional, HP, bedgraph - stub") {

config "./nextflow.traditional_hp_bedgraph.config"
options "-stub"
Expand All @@ -357,7 +366,8 @@ nextflow_process {
]
input[1] = [
[ id: 'test_ref' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
]
input[2] = Channel.of('chr22\t0\t1000')
.collectFile(name: 'chr22.bed', newLine: true)
Expand Down
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