Skip to content

Update all modules #39

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
famosab merged 5 commits into from
Dec 11, 2025
Merged

Update all modules #39

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
0c4f0aa
Update all modules
famosab Dec 10, 2025
2c33981
Update snaps
famosab Dec 10, 2025
244e6af
Update Changelog
famosab Dec 10, 2025
1151b85
Language Server Stuff
famosab Dec 10, 2025
b6084d1
Resolve comments
famosab Dec 11, 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
44 changes: 22 additions & 22 deletions conf/base.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,9 @@

process {

cpus = { 1 * task.attempt }
memory = { 6.GB * task.attempt }
time = { 4.h * task.attempt }
cpus = { 1 * task.attempt }
memory = { 6.GB * task.attempt }
time = { 4.h * task.attempt }

errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
maxRetries = 1
Expand All @@ -23,43 +23,43 @@ process {
// These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
// If possible, it would be nice to keep the same label naming convention when
// adding in your local modules too.
withLabel:error_ignore {
withLabel: error_ignore {
errorStrategy = 'ignore'
}
withLabel:error_retry {
withLabel: error_retry {
errorStrategy = 'retry'
maxRetries = 2
}
withLabel:process_single {
cpus = { 1 }
withLabel: process_single {
cpus = { 1 }
memory = { 6.GB * task.attempt }
time = { 4.h * task.attempt }
time = { 4.h * task.attempt }
}
withLabel:process_low {
cpus = { 2 * task.attempt }
withLabel: process_low {
cpus = { 2 * task.attempt }
memory = { 12.GB * task.attempt }
time = { 4.h * task.attempt }
time = { 4.h * task.attempt }
}
withLabel:process_medium {
cpus = { 6 * task.attempt }
withLabel: process_medium {
cpus = { 6 * task.attempt }
memory = { 36.GB * task.attempt }
time = { 8.h * task.attempt }
time = { 8.h * task.attempt }
}
withLabel:process_high {
cpus = { 12 * task.attempt }
withLabel: process_high {
cpus = { 12 * task.attempt }
memory = { 72.GB * task.attempt }
time = { 16.h * task.attempt }
time = { 16.h * task.attempt }
}
withLabel:process_long {
time = { 20.h * task.attempt }
withLabel: process_long {
time = { 20.h * task.attempt }
}
withLabel:process_high_memory {
withLabel: process_high_memory {
memory = { 200.GB * task.attempt }
}
withLabel:error_ignore {
withLabel: error_ignore {
errorStrategy = 'ignore'
}
withLabel:error_retry {
withLabel: error_retry {
errorStrategy = 'retry'
maxRetries = 2
}
Expand Down
478 changes: 239 additions & 239 deletions conf/igenomes.config
View file
Open in desktop

Large diffs are not rendered by default.

64 changes: 33 additions & 31 deletions conf/modules.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,19 +15,21 @@ process {
publishDir = [
path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
]

withName: BCFTOOLS_VIEW {
ext.args = { [ "",
params.filter ? "-f PASS": "",
"--output-type z"
].join(" ").trim() }
ext.args = {
[
"",
params.filter ? "-f PASS" : "",
"--output-type z",
].join(" ").trim()
}
}

withName: GUNZIP {
publishDir = [
//specify to avoid publishing, overwritten otherwise
publishDir = [
enabled: false
]
}
Expand All @@ -37,61 +39,61 @@ process {
[
path: { "${params.outdir}/liftover/lifted/" },
mode: params.publish_dir_mode,
pattern: "*.lifted.vcf.gz"
pattern: "*.lifted.vcf.gz",
],
[
path: { "${params.outdir}/liftover/unlifted/" },
mode: params.publish_dir_mode,
pattern: "*.unlifted.vcf.gz"
pattern: "*.unlifted.vcf.gz",
],
[
path: { "${params.outdir}/liftover/logs/" },
mode: params.publish_dir_mode,
pattern: "*.log"
]
pattern: "*.log",
],
]
}

withName: TABIX_TABIX {
publishDir = [
//specify to avoid publishing, overwritten otherwise
publishDir = [
enabled: false
]
}

withName: UNTAR {
publishDir = [
//specify to avoid publishing, overwritten otherwise
publishDir = [
enabled: false
]
}

withName: VCF2MAF {
ext.args = { [ "",
params.run_vep ? "" : "--inhibit-vep",
meta.normal_id ? "--normal-id ${meta.normal_id} --vcf-normal-id ${meta.vcf_normal_id}" : "",
meta.tumor_id ? "--tumor-id ${meta.tumor_id} --vcf-tumor-id ${meta.vcf_tumor_id}" : "",
"--retain-fmt AD,AF,DP,GQ,GT,STR",
"--retain-info AS_FilterStatus,AS_SB_TABLE,DP,MBQ,POPAF,STR,ANN,LOF,NMD",
"--retain-ann Allele,Consequence,IMPACT,SYMBOL,Gene,Feature_type,Feature,BIOTYPE,EXON,INTRON,HGVSc,HGVSp,CDNA_position,CDS_position,Protein_position,Amino_acids,Codons,Existing_variation,DISTANCE,STRAND,FLAGS,VARIANT_CLASS,SYMBOL_SOURCE,HGNC_ID,CANONICAL,MANE,MANE_SELECT,MANE_PLUS_CLINICAL,TSL,APPRIS,CCDS,ENSP,SWISSPROT,TREMBL,UNIPARC,UNIPROT_ISOFORM,GENE_PHENO,SIFT,PolyPhen,DOMAINS,miRNA,AF,AFR_AF,AMR_AF,EAS_AF,EUR_AF,SAS_AF,gnomADe_AF,gnomADe_AFR_AF,gnomADe_AMR_AF,gnomADe_ASJ_AF,gnomADe_EAS_AF,gnomADe_FIN_AF,gnomADe_MID_AF,gnomADe_NFE_AF,gnomADe_REMAINING_AF,gnomADe_SAS_AF,gnomADg_AF,gnomADg_AFR_AF,gnomADg_AMI_AF,gnomADg_AMR_AF,gnomADg_ASJ_AFIgnomADg_EAS_AF,gnomADg_FIN_AF,gnomADg_MID_AF,gnomADg_NFE_AF,gnomADg_REMAINING_AF,gnomADg_SAS_AF,gnomADg_EAS_AF_POPS,FREQS,CLIN_SIG,SOMATIC,PHENO,PUBMED,MOTIF_NAME,MOTIF_POS,HIGH_INF_POS,MOTIF_SCORE_CHANGE,TRANSCRIPTION_FACTORS",
"--any-allele",
"--ncbi-build ${params.genome.tokenize('.')[-1]}",
"--species homo_sapiens"
].join(" ").trim() }
ext.args = {
[
"",
params.run_vep ? "" : "--inhibit-vep",
meta.normal_id ? "--normal-id ${meta.normal_id} --vcf-normal-id ${meta.vcf_normal_id}" : "",
meta.tumor_id ? "--tumor-id ${meta.tumor_id} --vcf-tumor-id ${meta.vcf_tumor_id}" : "",
"--retain-fmt AD,AF,DP,GQ,GT,STR",
"--retain-info AS_FilterStatus,AS_SB_TABLE,DP,MBQ,POPAF,STR,ANN,LOF,NMD",
"--retain-ann Allele,Consequence,IMPACT,SYMBOL,Gene,Feature_type,Feature,BIOTYPE,EXON,INTRON,HGVSc,HGVSp,CDNA_position,CDS_position,Protein_position,Amino_acids,Codons,Existing_variation,DISTANCE,STRAND,FLAGS,VARIANT_CLASS,SYMBOL_SOURCE,HGNC_ID,CANONICAL,MANE,MANE_SELECT,MANE_PLUS_CLINICAL,TSL,APPRIS,CCDS,ENSP,SWISSPROT,TREMBL,UNIPARC,UNIPROT_ISOFORM,GENE_PHENO,SIFT,PolyPhen,DOMAINS,miRNA,AF,AFR_AF,AMR_AF,EAS_AF,EUR_AF,SAS_AF,gnomADe_AF,gnomADe_AFR_AF,gnomADe_AMR_AF,gnomADe_ASJ_AF,gnomADe_EAS_AF,gnomADe_FIN_AF,gnomADe_MID_AF,gnomADe_NFE_AF,gnomADe_REMAINING_AF,gnomADe_SAS_AF,gnomADg_AF,gnomADg_AFR_AF,gnomADg_AMI_AF,gnomADg_AMR_AF,gnomADg_ASJ_AFIgnomADg_EAS_AF,gnomADg_FIN_AF,gnomADg_MID_AF,gnomADg_NFE_AF,gnomADg_REMAINING_AF,gnomADg_SAS_AF,gnomADg_EAS_AF_POPS,FREQS,CLIN_SIG,SOMATIC,PHENO,PUBMED,MOTIF_NAME,MOTIF_POS,HIGH_INF_POS,MOTIF_SCORE_CHANGE,TRANSCRIPTION_FACTORS",
"--any-allele",
"--ncbi-build ${params.genome.tokenize('.')[-1]}",
"--species homo_sapiens",
].join(" ").trim()
}
publishDir = [
path: { "${params.outdir}/maf" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
]
}

withName: 'MULTIQC' {
ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
withName: MULTIQC {
ext.args = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' }
publishDir = [
path: { "${params.outdir}/multiqc" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
]
}

}
13 changes: 6 additions & 7 deletions conf/test.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ process {
resourceLimits = [
cpus: 4,
memory: '15.GB',
time: '1.h'
time: '1.h',
]
}

Expand All @@ -23,10 +23,9 @@ params {
config_profile_description = 'Minimal test dataset to check pipeline function'

// Input data
input = "${projectDir}/tests/samplesheets/samplesheet.csv"
fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
intervals = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.bed'
genome = 'GATK.GRCh38'
filter = false

input = "${projectDir}/tests/samplesheets/samplesheet.csv"
fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
intervals = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.bed'
genome = 'GATK.GRCh38'
filter = false
}
111 changes: 48 additions & 63 deletions main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,46 @@ include { VCFTOMAF } from './workflows/vcftomaf'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

workflow {
//
// SUBWORKFLOW: Run initialisation tasks
//
PIPELINE_INITIALISATION(
params.version,
params.validate_params,
params.monochrome_logs,
args,
params.outdir,
params.input,
params.help,
params.help_full,
params.show_hidden,
)

//
// WORKFLOW: Run main workflow
//
QBICPIPELINES_VCFTOMAF(
PIPELINE_INITIALISATION.out.samplesheet
)

//
PIPELINE_COMPLETION(
params.email,
params.email_on_fail,
params.plaintext_email,
params.outdir,
params.monochrome_logs,
params.hook_url,
QBICPIPELINES_VCFTOMAF.out.multiqc_report,
)
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand All @@ -28,97 +68,42 @@ include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_vcft
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow QBICPIPELINES_VCFTOMAF {

take:
samplesheet // channel: samplesheet read in from --input

main:

//
// SET PARAMETERS
//
params.fasta = getGenomeAttribute('fasta')
params.dict = getGenomeAttribute('dict')

// Extra files
intervals = params.intervals ? Channel.fromPath(params.intervals).collect() : Channel.value([])
liftover_chain = params.liftover_chain ? Channel.fromPath(params.liftover_chain).collect() : Channel.value([])
intervals = params.intervals ? channel.fromPath(params.intervals).collect() : channel.value([])
liftover_chain = params.liftover_chain ? channel.fromPath(params.liftover_chain).collect() : channel.value([])

// FASTA
fasta = params.fasta ? Channel.fromPath(params.fasta).collect() : Channel.value([])
dict = params.dict ? Channel.fromPath(params.dict).collect() : Channel.empty()

// Genome version
genome = params.genome ?: Channel.empty()
fasta = params.fasta ? channel.fromPath(params.fasta).collect() : channel.value([])
dict = params.dict ? channel.fromPath(params.dict).collect() : channel.empty()

// VEP cache
vep_cache = params.vep_cache ? Channel.fromPath(params.vep_cache).collect() : Channel.value([])
vep_cache_unpacked = Channel.value([])

vep_cache = params.vep_cache ? channel.fromPath(params.vep_cache).collect() : channel.value([])
vep_cache_unpacked = channel.value([])

//
// WORKFLOW: Run pipeline
//

VCFTOMAF (
VCFTOMAF(
samplesheet,
intervals,
fasta,
dict,
liftover_chain,
genome,
vep_cache,
vep_cache_unpacked
vep_cache_unpacked,
)

emit:
multiqc_report = VCFTOMAF.out.multiqc_report // channel: /path/to/multiqc_report.html
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

workflow {

main:
//
// SUBWORKFLOW: Run initialisation tasks
//
PIPELINE_INITIALISATION (
params.version,
params.validate_params,
params.monochrome_logs,
args,
params.outdir,
params.input,
params.help,
params.help_full,
params.show_hidden
)

//
// WORKFLOW: Run main workflow
//
QBICPIPELINES_VCFTOMAF (
PIPELINE_INITIALISATION.out.samplesheet
)

//
PIPELINE_COMPLETION (
params.email,
params.email_on_fail,
params.plaintext_email,
params.outdir,
params.monochrome_logs,
params.hook_url,
QBICPIPELINES_VCFTOMAF.out.multiqc_report
)
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
Loading
⚡