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Replace several skip_<tools> parameters with a single skip_tools parameter #690

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Merged
merged 12 commits into from
Mar 26, 2025
Merged

Replace several skip_<tools> parameters with a single skip_tools parameter #690

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779cfee
haplogrep3 and fastp
ramprasadn Mar 21, 2025
4f52af0
Merge branch 'dev' of github.com:nf-core/raredisease into skip_tools
ramprasadn Mar 21, 2025
cd3f141
gens and peddy
ramprasadn Mar 21, 2025
05ee466
smncopynumbercaller
ramprasadn Mar 21, 2025
a2d5f85
germlinecnvcaller
ramprasadn Mar 21, 2025
182ae32
vcf2cytosure
ramprasadn Mar 21, 2025
a2de255
add fastqc
ramprasadn Mar 21, 2025
d26ad36
remove samplesheet
ramprasadn Mar 21, 2025
976686c
fix syntax
ramprasadn Mar 24, 2025
4550a3d
update conditional
ramprasadn Mar 24, 2025
901424a
Merge branch 'dev' of github.com:nf-core/raredisease into skip_tools
ramprasadn Mar 24, 2025
cc9ca05
update citations
ramprasadn Mar 24, 2025
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12 changes: 9 additions & 3 deletions CHANGELOG.md
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Expand Up @@ -22,9 +22,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Parameters

| Old parameter | New parameter |
| ------------- | ------------- |
| | |
| Old parameter | New parameter |
| ------------------------ | ------------- |
| skip_haplogrep3 | skip_tools |
| skip_fastp | |
| skip_gens | |
| skip_germlinecnvcaller | |
| skip_peddy | |
| skip_smncopynumbercaller | |
| skip_vcf2cytosure | |
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add skip_fastqc

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skip_fastqc doesn't exist actually. I just added that functionality to skip_tools 😅


### Tool updates

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5 changes: 1 addition & 4 deletions conf/test.config
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Expand Up @@ -27,12 +27,9 @@ params {
mito_name = 'MT'

// analysis params
skip_germlinecnvcaller = true
skip_mt_annotation = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip annotation on Github CI
skip_mt_subsample = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip subsample on Github CI
skip_peddy = true
skip_haplogrep3 = true

skip_tools = 'gens,haplogrep3,peddy,germlinecnvcaller'
// Input data

input = params.pipelines_testdata_base_path + 'raredisease/testdata/samplesheet_fq_spring.csv'
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4 changes: 1 addition & 3 deletions conf/test_bam.config
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Expand Up @@ -28,11 +28,9 @@ params {
ngsbits_samplegender_method = 'sry'

// analysis params
skip_germlinecnvcaller = true
skip_mt_annotation = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip annotation on Github CI
skip_mt_subsample = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip subsample on Github CI
skip_peddy = true
skip_haplogrep3 = true
skip_tools = 'gens,haplogrep3,peddy,germlinecnvcaller'


// Input data
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5 changes: 2 additions & 3 deletions conf/test_full.config
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Expand Up @@ -20,11 +20,10 @@ params {
mito_name = 'MT'

// analysis params
skip_germlinecnvcaller = true
skip_peddy = true
skip_tools = 'gens,haplogrep3,peddy,germlinecnvcaller'

// Input data
input = params.pipelines_testdata_base_path + 'raredisease/testdata/samplesheet_trio.csv'
input = params.pipelines_testdata_base_path + 'raredisease/testdata/samplesheet_trio.csv'

// Genome references
fasta = params.pipelines_testdata_base_path + 'raredisease/reference/reference.fasta'
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3 changes: 1 addition & 2 deletions conf/test_one_sample.config
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Expand Up @@ -27,10 +27,9 @@ params {
mito_name = 'MT'

// analysis params
skip_germlinecnvcaller = true
skip_mt_annotation = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip annotation on Github CI
skip_mt_subsample = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip subsample on Github CI
skip_peddy = true
skip_tools = 'gens,haplogrep3,peddy,germlinecnvcaller'

// Input data
input = params.pipelines_testdata_base_path + 'raredisease/testdata/samplesheet_single.csv'
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4 changes: 1 addition & 3 deletions conf/test_sentieon.config
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Expand Up @@ -24,9 +24,7 @@ params {
mito_name = 'MT'

// analysis params
skip_germlinecnvcaller = true
skip_peddy = true
skip_haplogrep3 = true
skip_tools = 'gens,haplogrep3,peddy,germlinecnvcaller'

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_trio.csv'
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4 changes: 2 additions & 2 deletions docs/output.md
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Expand Up @@ -310,7 +310,7 @@ The pipeline performs variant calling using [Sentieon DNAscope](https://support.

#### SVDB merge

[SVDB merge](https://github.com/J35P312/SVDB#merge) is used to merge the variant calls from GATK's GermlineCNVCaller (only if `skip_germlinecnvcaller` is set to false), Manta, and TIDDIT. Output files are published in the output folder.
[SVDB merge](https://github.com/J35P312/SVDB#merge) is used to merge the variant calls from GATK's GermlineCNVCaller (only if `skip_tools` doesn't include germlinecnvcaller), Manta, and TIDDIT. Output files are published in the output folder.

<details markdown="1">
<summary>Output files</summary>
Expand Down Expand Up @@ -616,7 +616,7 @@ Provided a truth set, SNVs can be evaluated using RTG Tools' vcfeval engine. Out

### Gens

The sequencing data can be prepared for visualization of CNVs in [Gens](https://github.com/Clinical-Genomics-Lund/gens). This subworkflow is turned off by default. You can activate it by supplying the option `--skip_gens false`. You can read more about how to setup Gens [here](https://github.com/Clinical-Genomics-Lund/gens).
The sequencing data can be prepared for visualization of CNVs in [Gens](https://github.com/Clinical-Genomics-Lund/gens). You can turn it off by supplying the option `--skip_tools gens`. You can read more about how to setup Gens [here](https://github.com/Clinical-Genomics-Lund/gens).

<details markdown="1">
<summary>Output files</summary>
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2 changes: 1 addition & 1 deletion docs/usage.md
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Expand Up @@ -354,7 +354,7 @@ We use CADD only to annotate small indels. To annotate SNVs with precomputed CAD

##### 13. Prepare data for CNV visualisation in Gens

Optionally the read data can be prepared for CNV visualization in [Gens](https://github.com/Clinical-Genomics-Lund/gens). This subworkflow is turned off by default. You can activate it by supplying the option `--skip_gens false`.
Optionally the read data can be prepared for CNV visualization in [Gens](https://github.com/Clinical-Genomics-Lund/gens). You can turn it off it by supplying the option `--skip_tools gens`.

| Mandatory | Optional |
| ------------------------------ | -------- |
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8 changes: 1 addition & 7 deletions nextflow.config
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Expand Up @@ -30,23 +30,17 @@ params {
run_rtgvcfeval = false
save_mapped_as_cram = false
scatter_count = 20
skip_fastp = false
skip_gens = true
skip_germlinecnvcaller = false
skip_haplogrep3 = false
skip_peddy = false
skip_tools = null
skip_me_calling = false
skip_me_annotation = false
skip_mt_annotation = false
skip_repeat_annotation = false
skip_repeat_calling = false
skip_smncopynumbercaller = false
skip_snv_annotation = false
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are you planning to add another skip parameter for the remaining params? Or you plan to infer it from samplesheet in future?

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Other skip parameters turn off entire subworkflows so it would be misleading to combine them under skip_tools. So as of now, I don't plan on combining them with skip_tools:)

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himm, maybe having them combine into --skip_subworkflows, or adding like --steps "snvcalling, snvannotation,repeat_annotation" might work.. I guess I am into clustering :)

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That's a good idea. I will do that in a different PR.

skip_snv_calling = false
skip_sv_annotation = false
skip_sv_calling = false
skip_mt_subsample = false
skip_vcf2cytosure = true
skip_vep_filter = false
cadd_resources = null
platform = 'illumina'
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42 changes: 6 additions & 36 deletions nextflow_schema.json
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Expand Up @@ -549,31 +549,6 @@
"description": "Number of intervals to split your genome into (used to parallelize annotations)",
"fa_icon": "fas fa-less-than"
},
"skip_fastp": {
"type": "boolean",
"description": "Specifies whether or not to skip trimming with fastp.",
"fa_icon": "fas fa-toggle-on"
},
"skip_gens": {
"type": "boolean",
"description": "Specifies whether or not to skip gens preprocessing subworkflow.",
"fa_icon": "fas fa-toggle-on"
},
"skip_germlinecnvcaller": {
"type": "boolean",
"description": "Specifies whether or not to skip CNV calling using GATK's GermlineCNVCaller",
"fa_icon": "fas fa-toggle-on"
},
"skip_haplogrep3": {
"type": "boolean",
"description": "Specifies whether or not to skip haplogrep3.",
"fa_icon": "fas fa-toggle-on"
},
"skip_peddy": {
"type": "boolean",
"description": "Specifies whether or not to skip peddy.",
"fa_icon": "fas fa-toggle-on"
},
"skip_me_calling": {
"type": "boolean",
"description": "Specifies whether or not to skip calling mobile elements, and the subsequent annotation step.",
Expand Down Expand Up @@ -604,11 +579,6 @@
"description": "Specifies whether or not to skip calling of repeat expansions.",
"fa_icon": "fas fa-toggle-on"
},
"skip_smncopynumbercaller": {
"type": "boolean",
"description": "Specifies whether or not to skip smncopynumbercaller.",
"fa_icon": "fas fa-toggle-on"
},
"skip_snv_annotation": {
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might make sense to add more general skip option here? like skip "annotation"? I think it would be a rare case to have lets say snvannotation on while svannotaton off?

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Depends on the use case, I believe. There are scenarios where someone might have updated databases for SNVs, and in such cases, they might not want to run SV annotation.

"type": "boolean",
"description": "Specifies whether or not to skip annotate SNV subworkflow.",
Expand All @@ -629,12 +599,12 @@
"description": "Specifies whether or not to skip nuclear and mitochondrial SV calling and annotation.",
"fa_icon": "fas fa-toggle-on"
},
"skip_vcf2cytosure": {
"type": "boolean",
"default": true,
"description": "Specifies whether or not to skip the vcf2cytosure subworkflow",
"help_text": "vcf2cytosure can generate CGH files from a structural variant VCF file that can be analysed in the CytoSure interpretation software. Cut-offs for allele frequencies and bin sizes can be modified in the config file. Turned off by default.",
"fa_icon": "fas fa-toggle-on"
"skip_tools": {
"type": "string",
"fa_icon": "fas fa-forward",
"description": "Disable specified tools.",
"help_text": "Multiple tools can be specified, separated by commas.\n\n> **NB** `--skip_tools baserecalibrator_report` is actually just not saving the reports.\n> **NB** `--skip_tools markduplicates_report` does not skip `MarkDuplicates` but prevent the collection of duplicate metrics that slows down performance.",
"pattern": "^((fastp|gens|germlinecnvcaller|haplogrep3|peddy|smncopynumbercaller|vcf2cytosure|fastqc)?,?)*(?<!,)$"
},
"skip_vep_filter": {
"type": "boolean",
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2 changes: 1 addition & 1 deletion subworkflows/local/align.nf
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Expand Up @@ -49,7 +49,7 @@ workflow ALIGN {
ch_sentieon_bai = Channel.empty()
ch_versions = Channel.empty()

if (!params.skip_fastp) {
if (!(params.skip_tools && params.skip_tools.split(',').contains('fastp'))) {
FASTP (ch_reads, [], false, false, false)
ch_reads = FASTP.out.reads
ch_versions = ch_versions.mix(FASTP.out.versions)
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2 changes: 1 addition & 1 deletion subworkflows/local/annotate_mt_snvs.nf
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Expand Up @@ -100,7 +100,7 @@ workflow ANNOTATE_MT_SNVS {
TABIX_TABIX_VEP_MT(ENSEMBLVEP_MT.out.vcf)

// Running haplogrep3
if (!params.skip_haplogrep3) {
if (!(params.skip_tools && params.skip_tools.split(',').contains('haplogrep3'))) {
HAPLOGREP3_CLASSIFY_MT(ch_haplogrep_in)
ch_haplog = HAPLOGREP3_CLASSIFY_MT.out.txt
ch_versions = ch_versions.mix(HAPLOGREP3_CLASSIFY_MT.out.versions)
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4 changes: 2 additions & 2 deletions subworkflows/local/call_structural_variants.nf
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Expand Up @@ -57,7 +57,7 @@ workflow CALL_STRUCTURAL_VARIANTS {
ch_versions = ch_versions.mix(CALL_SV_CNVNATOR.out.versions)
}

if (!params.skip_germlinecnvcaller) {
if (!(params.skip_tools && params.skip_tools.split(',').contains('germlinecnvcaller'))) {
CALL_SV_GERMLINECNVCALLER (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_readcount_intervals, ch_genome_dictionary, ch_ploidy_model, ch_gcnvcaller_model, ch_case_info)
.genotyped_filtered_segments_vcf
.collect{it[1]}
Expand All @@ -72,7 +72,7 @@ workflow CALL_STRUCTURAL_VARIANTS {
}

//merge
if (params.skip_germlinecnvcaller) {
if (params.skip_tools && params.skip_tools.split(',').contains('germlinecnvcaller')) {
if (params.analysis_type.equals("wgs")) {
tiddit_vcf
.combine(manta_vcf)
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