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add cancer splicing lib to starfusion ref #610

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add cancer splicing lib to starfusion ref #610

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a317529
add cancer splicing lib to starfusion ref
nvnieuwk Jan 21, 2025
43b6045
update changelog
nvnieuwk Jan 21, 2025
472da39
update prepgenomelib resources
nvnieuwk Jan 21, 2025
0915989
fix stub test snapshot
nvnieuwk Jan 21, 2025
10d431d
add param instead of hardcoded url
nvnieuwk Jan 22, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -28,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Add nf-test to local subworkflow: `FUSIONCATCHER_WORKFLOW` [#591](https://github.com/nf-core/rnafusion/pull/591)
- Add nf-test to local subworkflow: `STARFUSION_WORKFLOW`. [#597](https://github.com/nf-core/rnafusion/pull/597)
- Add nf-test to local module: `FUSIONINSPECTOR`. [#601](https://github.com/nf-core/rnafusion/pull/601)
- Added `CTATSPLICING_PREPGENOMELIB` to update the starfusion genome library directory with a cancer splicing index. [#610](https://github.com/nf-core/rnafusion/pull/610)

### Changed

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14 changes: 13 additions & 1 deletion conf/modules.config
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Expand Up @@ -360,10 +360,22 @@ process {
]
}

withName: 'NFCORE_RNAFUSION:BUILD_REFERENCES:STARFUSION_BUILD' {
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withName: 'STARFUSION_BUILD' {
cpus = { 24 * task.attempt }
memory = { 100.GB * task.attempt }
time = { 2.d * task.attempt }
publishDir = [
enabled: !params.ctatsplicing && !params.all,
path: { "${params.genomes_base}/starfusion" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
]
ext.args = "--max_readlength ${params.read_length} --human_gencode_filter"
}

withName: 'CTATSPLICING_PREPGENOMELIB' {
cpus = { 1 * task.attempt }
memory = { 20.GB * task.attempt }
publishDir = [
path: { "${params.genomes_base}/starfusion" },
mode: params.publish_dir_mode,
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44 changes: 44 additions & 0 deletions modules/local/ctatsplicing/prepgenomelib/main.nf
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Could you add the module's test ? :)

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Right! I forgot thanks for the reminder :)

Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
process CTATSPLICING_PREPGENOMELIB {
tag "$meta.id"
label 'process_single'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://data.broadinstitute.org/Trinity/CTAT_SINGULARITY/CTAT-SPLICING/ctat_splicing.v0.0.2.simg' :
'docker.io/trinityctat/ctat_splicing:0.0.2' }"

input:
tuple val(meta), path(genome_lib)
path(cancer_intron_tsv)

output:
tuple val(meta), path(genome_lib, includeInputs:true), emit: reference
path "versions.yml" , emit: versions

script:
def VERSION = '0.0.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
/usr/local/src/CTAT-SPLICING/prep_genome_lib/ctat-splicing-lib-integration.py \\
--cancer_introns_tsv cancer_introns.*.tsv.gz \\
--genome_lib_dir $genome_lib

cat <<-END_VERSIONS > versions.yml
"${task.process}":
ctat-splicing: $VERSION
END_VERSIONS
"""

stub:
def VERSION = '0.0.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
touch $genome_lib/refGene.bed
touch $genome_lib/refGene.sort.bed.gz
touch $genome_lib/refGene.sort.bed.gz.tbi
mkdir $genome_lib/cancer_splicing_lib
touch $genome_lib/cancer_splicing_lib/cancer_splicing.idx

cat <<-END_VERSIONS > versions.yml
"${task.process}":
ctat-splicing: $VERSION
END_VERSIONS
"""
}
2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -90,7 +90,7 @@ params {
starfusion_ref = "${params.genomes_base}/starfusion/ctat_genome_lib_build_dir"
starindex_ref = "${params.genomes_base}/star"
fusionreport_ref = "${params.genomes_base}/fusion_report_db"

ctatsplicing_cancer_introns = "https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/CANCER_SPLICING_LIB_SUPPLEMENT/cancer_introns.GRCh38.Jun232020.tsv.gz"

// Internal file presence checks
salmon_index_stub_check = "${params.genomes_base}/salmon/salmon/complete_ref_lens.bin"
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7 changes: 7 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -247,6 +247,13 @@
"fa_icon": "far fa-file-code",
"description": "Path to file in starfusion references"
},
"ctatsplicing_cancer_introns": {
"type": "string",
"format": "file-path",
"exists": true,
"description": "Path to the cancer introns CSV file to create the CTAT-SPLICING reference with",
"default": "https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/CANCER_SPLICING_LIB_SUPPLEMENT/cancer_introns.GRCh38.Jun232020.tsv.gz"
},
"starindex": {
"type": "boolean",
"fa_icon": "far fa-file-code",
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12 changes: 11 additions & 1 deletion subworkflows/local/build_references.nf
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Expand Up @@ -11,6 +11,7 @@ include { HGNC_DOWNLOAD } from '../../modules/local/hgnc/main'
include { STARFUSION_BUILD } from '../../modules/local/starfusion/build/main'
include { GTF_TO_REFFLAT } from '../../modules/local/uscs/custom_gtftogenepred/main'
include { GET_RRNA_TRANSCRIPTS } from '../../modules/local/get_rrna_transcript/main'
include { CTATSPLICING_PREPGENOMELIB } from '../../modules/local/ctatsplicing/prepgenomelib/main.nf'

/*
========================================================================================
Expand Down Expand Up @@ -142,7 +143,16 @@ workflow BUILD_REFERENCES {
!file(params.starfusion_ref_stub_check).exists() || file(params.starfusion_ref_stub_check).isEmpty() )) {
STARFUSION_BUILD(ch_fasta, ch_gtf, params.fusion_annot_lib, params.species)
ch_versions = ch_versions.mix(STARFUSION_BUILD.out.versions)
ch_starfusion_ref = STARFUSION_BUILD.out.reference
if (params.ctatsplicing || params.all) {
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Suggested change
if (params.ctatsplicing || params.all) {
if (params.ctatsplicing) {

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The params.all is in the outer if clause:

 if ((params.starfusion || params.all) &&
            (!file(params.starfusion_ref).exists() || file(params.starfusion_ref).isEmpty() ||
            !file(params.starfusion_ref_stub_check).exists() || file(params.starfusion_ref_stub_check).isEmpty() )) {
            STARFUSION_BUILD(ch_fasta, ch_gtf, params.fusion_annot_lib, params.species)

I think that is why the test_build is failing. It is not populating the ch_starfusion_ref with CTATSPLICING_PREPGENOMELIB.out.reference or STARFUSION_BUILD.out.reference

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Hmm but the ctatsplicing reference creation will not run if --all is supplied this way?

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I think it is difficult to differentiate which is the default here. If --all is supplied, should ch_starfusion_ref produce STARFUSION_BUILD.out.reference or CTATSPLICING_PREPGENOMELIB.out.reference?

Before adding your new module CTATSPLICING_PREPGENOMELIB, the default for --all was to use the STARFUSION_BUILD.out.reference but now it will always default to CTATSPLICING_PREPGENOMELIB.out.reference.

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Hi yeah sorry for the confusion:
CTATSPLICING_PREPGENOMELIB.out.reference basically is the STARFUSION reference with some added extra files to the ctatsplicing folder inside of it. So this does not emit a different reference but an expanded reference

CTATSPLICING_PREPGENOMELIB(
STARFUSION_BUILD.out.reference,
params.ctatsplicing_cancer_introns
)
ch_versions = ch_versions.mix(CTATSPLICING_PREPGENOMELIB.out.versions)
ch_starfusion_ref = CTATSPLICING_PREPGENOMELIB.out.reference
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} else {
ch_starfusion_ref = STARFUSION_BUILD.out.reference
}
}
else {
ch_starfusion_ref = Channel.fromPath(params.starfusion_ref)
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