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IGV Snapshot module #125

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e08270f
init module
Aug 6, 2024
e917939
name corrections
Aug 6, 2024
07387e8
fixing snapshot and names
Aug 6, 2024
467ed1a
Update test.yml
Aug 7, 2024
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2 changes: 2 additions & 0 deletions .github/workflows/test.yml
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Expand Up @@ -416,6 +416,8 @@ jobs:
tags: salmon/quant
- profile: "conda"
tags: rediscoverte
- profile: "conda"
tags: igv/snapshot

env:
NXF_ANSI_LOG: false
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9 changes: 9 additions & 0 deletions modules/msk/igv/snapshot/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
name: "igv_snapshot"
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- "bioconda::igv=2.17.4"
57 changes: 57 additions & 0 deletions modules/msk/igv/snapshot/main.nf
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process IGV_SNAPSHOT {
tag "$meta.id"
label 'process_single'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'ghcr.io/msk-access/igv_snapshot:0.0.1':
'ghcr.io/msk-access/igv_snapshot:0.0.1' }"

input:
tuple val(meta), path(bam), path(bai), path(variant_file)

output:

tuple val(meta), path("**igv_output/*"), emit: igv_screenshots
path "versions.yml" , emit: versions

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

script:
def args = task.ext.args ?: ""
def prefix = task.ext.prefix ?: "${meta.id}"
def bed_name = prefix ? "${prefix}.bed": "variant.bed"
def out = prefix ? "${prefix}_igv_output": "igv_output"
def genome = task.ext.genome ? "-g ${task.ext.genome}" : ""
"""
igv run_screenshot \\
--input-files $bam \\
--annotated-variant-file $variant_file \\
-t $prefix \\
-o $out \\
-r $bed_name \\
$genome

cat <<-END_VERSIONS > versions.yml
"${task.process}":
igv: \$(igv --version)
END_VERSIONS
"""

stub:
def args = task.ext.args ?: ""
def prefix = task.ext.prefix ?: "${meta.id}"
def bed_name = prefix ? "${prefix}.bed": "variant.bed"
def out = prefix ? "${prefix}_igv_output": "igv_output"
"""
mkdir $out
touch $out/test.png
touch $out/test.bat

cat <<-END_VERSIONS > versions.yml
"${task.process}":
igv: \$(igv --version)
END_VERSIONS
"""
}
62 changes: 62 additions & 0 deletions modules/msk/igv/snapshot/meta.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "igv_snapshot"
description: a module to run IGV screenshot
keywords:
- sort
- example
- genomics
tools:
- "igv":
description: "Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations."
homepage: "https://igv.org/"
documentation: "https://igv.org/doc/desktop/#QuickStart/"
tool_dev_url: "https://github.com/igvteam/igv"
licence: ["MIT"]
- "igv snapshot":
description: "A python package to generate and execute IGV screenshot script."
documentation: "https://github.com/msk-access/igv_snapshot/blob/main/README.md"
tool_dev_url: "https://github.com/msk-access/igv_snapshot"
licence: ["MIT"]

input:
# Only when we have meta
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`
- bam:
type: file
description: BAM file with index.
pattern: "*.{bam,cram,sam}"
- bai:
type: file
description: BAM file index
pattern: "*.{bai}"
- variant_file:
type: file
description: Variant file of input BAM.
pattern: "*.{maf,vcf}"

output:
#Only when we have meta
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`

- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- igv_screenshots:
type: directory
description: directory containing IGV screenshot for provided sample, and the bat script used to generate the screenshots.
pattern: "**igv_output/*"

authors:
- "@buehlere"
maintainers:
- "@buehlere"
64 changes: 64 additions & 0 deletions modules/msk/igv/snapshot/tests/main.nf.test
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nextflow_process {

name "Test Process IGV_SNAPSHOT"
script "../main.nf"
process "IGV_SNAPSHOT"

tag "modules"
tag "modules_nfcore"
tag "modules_msk"
tag "igv"
tag "igv/snapshot"

test("chr22 - bam, vcf") {

when {
process {
"""
input[0] = [
[ id:'C-9M47TU-L001-d'], // meta map
file(params.test_data_mskcc['chr22']['chr22bam'], checkIfExists: true),
file(params.test_data_mskcc['chr22']['chr22bam_bai'], checkIfExists: true),
file(params.test_data_mskcc['chr22']['chr22vcf'], checkIfExists: true)

]
"""
}
}

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

}

test("chr22 - bam, vcf - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'C-9M47TU-L001-d'], // meta map
file(params.test_data_mskcc['chr22']['chr22bam'], checkIfExists: true),
file(params.test_data_mskcc['chr22']['chr22bam_bai'], checkIfExists: true),
file(params.test_data_mskcc['chr22']['chr22vcf'], checkIfExists: true)
]
"""
}
}

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

}

}
82 changes: 82 additions & 0 deletions modules/msk/igv/snapshot/tests/main.nf.test.snap
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{
"chr22 - bam, vcf - stub": {
"content": [
{
"0": [
[
{
"id": "C-9M47TU-L001-d"
},
[
"test.bat:md5,d41d8cd98f00b204e9800998ecf8427e",
"test.png:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"1": [
"versions.yml:md5,870a90d9f64f5a5f5ec4cd474d69027c"
],
"igv_screenshots": [
[
{
"id": "C-9M47TU-L001-d"
},
[
"test.bat:md5,d41d8cd98f00b204e9800998ecf8427e",
"test.png:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"versions": [
"versions.yml:md5,870a90d9f64f5a5f5ec4cd474d69027c"
]
}
],
"timestamp": "2024-08-06T17:08:44.477177"
},
"chr22 - bam, vcf": {
"content": [
{
"0": [
[
{
"id": "C-9M47TU-L001-d"
},
[
"22_22127176_22127176.png:md5,fd9de31a371db4523f8a0982df749a09",
"22_41565827_41565827.png:md5,1904ecf0b28baeee6e14e78543052a17",
"22_41566406_41566406.png:md5,c77c48716ed2272f45b49c7852a74705",
"22_41566413_41566413.png:md5,bfaf4189292aa0495e51c26ea33f64f7",
"22_41566595_41566595.png:md5,2fca6b6e75fd4c533fb512d0cd11941b",
"22_41566657_41566657.png:md5,fd49c1c6439206da9c15595921392d29",
"IGV_snapshots.bat:md5,d2eaf7a013f62e5fe07f8a0ddf459ace"
]
]
],
"1": [
"versions.yml:md5,870a90d9f64f5a5f5ec4cd474d69027c"
],
"igv_screenshots": [
[
{
"id": "C-9M47TU-L001-d"
},
[
"22_22127176_22127176.png:md5,fd9de31a371db4523f8a0982df749a09",
"22_41565827_41565827.png:md5,1904ecf0b28baeee6e14e78543052a17",
"22_41566406_41566406.png:md5,c77c48716ed2272f45b49c7852a74705",
"22_41566413_41566413.png:md5,bfaf4189292aa0495e51c26ea33f64f7",
"22_41566595_41566595.png:md5,2fca6b6e75fd4c533fb512d0cd11941b",
"22_41566657_41566657.png:md5,fd49c1c6439206da9c15595921392d29",
"IGV_snapshots.bat:md5,d2eaf7a013f62e5fe07f8a0ddf459ace"
]
]
],
"versions": [
"versions.yml:md5,870a90d9f64f5a5f5ec4cd474d69027c"
]
}
],
"timestamp": "2024-08-06T17:08:31.32318"
}
}
2 changes: 2 additions & 0 deletions modules/msk/igv/snapshot/tests/tags.yml
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igv/snapshot:
- "modules/msk/igv/snapshot/**"
3 changes: 3 additions & 0 deletions tests/config/test_data.config
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Expand Up @@ -725,6 +725,9 @@ params {
dbsnp_138_b37_chr17_vcf_gz_tbi = "${params.test_data_base_msk}/hg37/genomic_reference/GRCH37/vcf/dbsnp_138.b37.chr17.vcf.gz.tbi"
}
'chr22' {
chr22bam = "${params.test_data_base_msk}/chr22/chr22/chr22.bam"
chr22bam_bai = "${params.test_data_base_msk}/chr22/chr22/chr22.bam.bai"
chr22vcf = "${params.test_data_base_msk}/chr22/chr22/chr22.vcf"
chr22maf = "${params.test_data_base_msk}/chr22/chr22/chr22.maf"
chr22mafstandard = "${params.test_data_base_msk}/chr22/chr22/chr22_standard.maf"
}
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