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Cnn reference #825

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merged 3 commits into from
Nov 11, 2022
Merged

Cnn reference #825

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6fd00e1
expose cnvkit reference as parameter
FriederikeHanssen Nov 10, 2022
bfaa982
don't compute reference if provided
FriederikeHanssen Nov 10, 2022
58bc75c
[automated] Fix linting with Prettier
nf-core-bot Nov 10, 2022
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2 changes: 1 addition & 1 deletion conf/modules/cnvkit.config
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Expand Up @@ -28,7 +28,7 @@ process {

withName: 'CNVKIT_REFERENCE' {
ext.prefix = "cnvkit"
ext.when = { params.tools && params.tools.split(',').contains('cnvkit') }
ext.when = { params.tools && params.tools.split(',').contains('cnvkit') && !params.cnvkit_reference }
publishDir = [
enabled: params.save_reference,
mode: params.publish_dir_mode,
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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -63,6 +63,7 @@ params {
cf_minqual = 0 // ControlFreec default values
cf_window = null // by default we are not using this in Control-FREEC
cf_chrom_len = null // by default we are using the fasta_fai. This can be used to circumvent this issue until there is a better option available upstream: https://github.com/nf-core/sarek/issues/670
cnvkit_reference = null // by default the reference is build from the fasta file
ignore_soft_clipped_bases = false // no --dont-use-soft-clipped-bases for GATK Mutect2
wes = false // Set to true, if data is exome/targeted sequencing data. Used to use correct models in various variant callers
joint_germline = false // g.vcf & joint germline calling are not run by default if HaplotypeCaller is selected
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8 changes: 7 additions & 1 deletion nextflow_schema.json
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Expand Up @@ -278,7 +278,7 @@
},
"cf_chrom_len": {
"type": "string",
"default": null,
"default": "None",
"fa_icon": "fas fa-ruler-horizontal",
"description": "Specify a custom chromosome length file.",
"help_text": "Control-FREEC requires a file containing all chromosome lenghts. By default the fasta.fai is used. If the fasta.fai file contains chromosomes not present in the intervals, it fails (see: https://github.com/BoevaLab/FREEC/issues/106).\n\nIn this case, a custom chromosome length can be specified. It must be of the same format as the fai, but only contain the relevant chromosomes.\n\n\n\n",
Expand Down Expand Up @@ -338,6 +338,12 @@
"help_text": "Details, see [ControlFREEC manual](http://boevalab.inf.ethz.ch/FREEC/tutorial.html).",
"hidden": true
},
"cnvkit_reference": {
"type": "string",
"default": null,
"fa_icon": "fas fa-file",
"help_text": "https://cnvkit.readthedocs.io/en/stable/pipeline.html?highlight=reference.cnn#batch"
},
"pon": {
"type": "string",
"fa_icon": "fas fa-file",
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4 changes: 3 additions & 1 deletion workflows/sarek.nf
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Expand Up @@ -18,6 +18,7 @@ def checkPathParamList = [
params.bwa,
params.bwamem2,
params.cf_chrom_len,
params.cnvkit_reference,
params.chr_dir,
params.dbnsfp,
params.dbnsfp_tbi,
Expand Down Expand Up @@ -372,7 +373,8 @@ workflow SAREK {

// Antitarget based reference for CNVKit
PREPARE_REFERENCE_CNVKIT(fasta, intervals_bed_combined)
cnvkit_reference = params.tools && params.tools.split(',').contains('cnvkit') ? PREPARE_REFERENCE_CNVKIT.out.cnvkit_reference : Channel.empty()
cnvkit_reference = params.tools && params.tools.split(',').contains('cnvkit') ? (params.cnvkit_reference ? Channel.fromPath(params.cnvkit_reference).collect() : PREPARE_REFERENCE_CNVKIT.out.cnvkit_reference) : Channel.empty()

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

// PREPROCESSING
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