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Update phylowgs multievolve to combine generation and write_results #248

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Update phylowgs multievolve to combine generation and write_results #248

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18 changes: 18 additions & 0 deletions modules/msk/phylowgs/multievolve/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -10,13 +10,17 @@ process PHYLOWGS_MULTIEVOLVE {

output:
tuple val(meta), path("chains/trees.zip") , emit: trees
tuple val(meta), path("*.summ.json.gz") , emit: summ
tuple val(meta), path("*.muts.json.gz") , emit: muts
tuple val(meta), path("*.mutass.zip") , emit: mutass
path "versions.yml" , emit: versions

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

script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

"""
Expand All @@ -26,6 +30,16 @@ process PHYLOWGS_MULTIEVOLVE {
--ssms ${ssm_data} \\
--cnvs ${cnv_data}

python2 \\
/usr/bin/phylowgs/write_results.py \\
${args2} \\
--include-ssm-names \\
${prefix} \\
chains/trees.zip \\
${prefix}.summ.json.gz \\
${prefix}.muts.json.gz \\
${prefix}.mutass.zip

cat <<-END_VERSIONS > versions.yml
"${task.process}":
phylowgs: \$PHYLOWGS_TAG
Expand All @@ -34,10 +48,14 @@ process PHYLOWGS_MULTIEVOLVE {

stub:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
mkdir chains
touch chains/trees.zip
touch ${prefix}.summ.json.gz
touch ${prefix}.muts.json.gz
touch ${prefix}.mutass.zip

cat <<-END_VERSIONS > versions.yml
"${task.process}":
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30 changes: 30 additions & 0 deletions modules/msk/phylowgs/multievolve/meta.yml
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Expand Up @@ -37,6 +37,36 @@ output:
type: file
description: Zip file containing the completed trees
pattern: "trees.zip"
- summ:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`
- "*.summ.json.gz":
type: file
description: Output file for JSON-formatted tree summaries
pattern: "*.summ.json.gz"
- muts:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`
- "*.muts.json.gz":
type: file
description: Output file for JSON-formatted list of mutations
pattern: "*.muts.json.gz"
- mutass:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`
- "*.mutass.zip":
type: file
description: Output file for JSON-formatted list of SSMs and CNVs
pattern: "*.mutass.zip"
- versions:
- versions.yml:
type: file
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10 changes: 8 additions & 2 deletions modules/msk/phylowgs/multievolve/tests/main.nf.test
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Expand Up @@ -28,7 +28,10 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(file(process.out.trees[0][1]).name).match() }
{ assert snapshot(file(process.out.trees[0][1]).name,
file(process.out.summ[0][1]).name,
file(process.out.muts[0][1]).name,
file(process.out.mutass[0][1]).name).match() }

)
}
Expand All @@ -54,7 +57,10 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(file(process.out.trees[0][1]).name,
file(process.out.summ[0][1]).name,
file(process.out.muts[0][1]).name,
file(process.out.mutass[0][1]).name).match() }

)
}
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47 changes: 18 additions & 29 deletions modules/msk/phylowgs/multievolve/tests/main.nf.test.snap
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@@ -1,39 +1,28 @@
{
"phylowgs_multievolve - zip": {
"content": [
"trees.zip"
"trees.zip",
"test.summ.json.gz",
"test.muts.json.gz",
"test.mutass.zip"
],
"timestamp": "2024-06-11T18:01:56.174868"
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.4"
},
"timestamp": "2026-06-04T11:48:34.725751"
},
"phylowgs_multievolve - zip - stub": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"trees.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,2eaafdf0e85898fdc2e5d40dbbfee2f7"
],
"trees": [
[
{
"id": "test",
"single_end": false
},
"trees.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,2eaafdf0e85898fdc2e5d40dbbfee2f7"
]
}
"trees.zip",
"test.summ.json.gz",
"test.muts.json.gz",
"test.mutass.zip"
],
"timestamp": "2024-06-11T18:02:03.678335"
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.4"
},
"timestamp": "2026-06-04T11:56:11.007179"
}
}
10 changes: 3 additions & 7 deletions subworkflows/msk/phylowgs/main.nf
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Expand Up @@ -36,16 +36,12 @@ workflow PHYLOWGS {

ch_versions = ch_versions.mix(PHYLOWGS_MULTIEVOLVE.out.versions)

PHYLOWGS_WRITERESULTS(PHYLOWGS_MULTIEVOLVE.out.trees)

ch_versions = ch_versions.mix(PHYLOWGS_WRITERESULTS.out.versions)


emit:

summ = PHYLOWGS_WRITERESULTS.out.summ // channel: [ val(meta), [ summ ] ]
muts = PHYLOWGS_WRITERESULTS.out.muts // channel: [ val(meta), [ muts ] ]
mutass = PHYLOWGS_WRITERESULTS.out.mutass // channel: [ val(meta), [ mutass ] ]
summ = PHYLOWGS_MULTIEVOLVE.out.summ // channel: [ val(meta), [ summ ] ]
muts = PHYLOWGS_MULTIEVOLVE.out.muts // channel: [ val(meta), [ muts ] ]
mutass = PHYLOWGS_MULTIEVOLVE.out.mutass // channel: [ val(meta), [ mutass ] ]
versions = ch_versions // channel: [ versions.yml ]
}

Expand Down
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