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Add variant caller to bcftools/vcftools + multiqc #618

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merged 17 commits into from
Jul 14, 2022
Merged

Add variant caller to bcftools/vcftools + multiqc #618

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2613281
add variant calling tool to vcf/bcftools + multiqc
SusiJo Jul 5, 2022
51b6cc6
Merge remote-tracking branch 'origin/dev' into bcftools_vcftools
SusiJo Jul 5, 2022
1e6704c
fix vcftools + fix typos
SusiJo Jul 6, 2022
2f21bcc
Merge remote-tracking branch 'origin/dev' into bcftools_vcftools
SusiJo Jul 6, 2022
173f7b6
fix mutect + gender
SusiJo Jul 6, 2022
71901f2
update multiqc module
SusiJo Jul 11, 2022
4e30625
update outputs varcallers + ci tests
SusiJo Jul 13, 2022
dcfd6cf
Merge remote-tracking branch 'origin/dev' into bcftools_vcftools
SusiJo Jul 13, 2022
2c2cbdb
update ymls
SusiJo Jul 13, 2022
a4b21dc
update ymls
SusiJo Jul 13, 2022
2f966b4
update yml
SusiJo Jul 13, 2022
1992894
update ascat yml
SusiJo Jul 13, 2022
4a5ed75
add suggested changes + rm view/dumps
SusiJo Jul 14, 2022
b952b6e
Merge remote-tracking branch 'origin/dev' into bcftools_vcftools
SusiJo Jul 14, 2022
e750e4e
revert back to former multiqc_config
SusiJo Jul 14, 2022
558ecd3
add description schema description for ascat
SusiJo Jul 14, 2022
43a0a52
rm unnecessary ext.args for multiqc
SusiJo Jul 14, 2022
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5 changes: 5 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -85,6 +85,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#630](https://github.com/nf-core/sarek/pull/630) - Update citations file
- [#632](https://github.com/nf-core/sarek/pull/632) - Update `snpEff` version to `5.1` and cache up to `105`
- [#632](https://github.com/nf-core/sarek/pull/632) - Update `VEP` version to `106.1` and cache up to `106`
- [#618](https://github.com/nf-core/sarek/pull/618) - Update `multiqc` module update test yml files
- [#618](https://github.com/nf-core/sarek/pull/618) - Update test yml files

### Fixed

Expand Down Expand Up @@ -126,6 +128,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#619](https://github.com/nf-core/sarek/pull/619) - Fix issue with checking samplesheet content with AWS
- [#628](https://github.com/nf-core/sarek/pull/628) - Fix issue with value converting to string before schema validation
- [#628](https://github.com/nf-core/sarek/pull/628) - Fix dbsnp check issue with `--step annotate`
- [#618](https://github.com/nf-core/sarek/pull/618) - Fix `bcftools/vcftools` sample labelling in multiqc report
- [#618](https://github.com/nf-core/sarek/pull/618) - Fix issue with tiddit [#621](https://github.com/nf-core/sarek/issues/621)
- [#618](https://github.com/nf-core/sarek/pull/618) - Fix channel issue with `targets.bed` in prepare_intervals

### Deprecated

Expand Down
75 changes: 43 additions & 32 deletions conf/modules.config
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Expand Up @@ -516,17 +516,18 @@ process{

// DEEPVARIANT
withName: 'MERGE_DEEPVARIANT_.*' {
ext.prefix = {"${meta.id}.deepvariant"}
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/deepvariant" },
pattern: "*{vcf.gz,vcf.gz.tbi}"
]
}
withName: 'MERGE_DEEPVARIANT_GVCF' {
ext.prefix = {"${meta.id}.g"}
ext.prefix = {"${meta.id}.deepvariant.g"}
}
withName: 'DEEPVARIANT' {
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}" : "${meta.id}_${intervals.simpleName}" }
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.deepvariant" : "${meta.id}.deepvariant.${intervals.simpleName}" }
ext.args = { params.wes ? "--model_type WES" : "--model_type WGS" }
ext.when = { params.tools && params.tools.contains('deepvariant') }
publishDir = [
Expand All @@ -537,6 +538,7 @@ process{
]
}
withName : 'TABIX_VC_DEEPVARIANT_.*' {
ext.prefix = {"${meta.id}.deepvariant"}
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/deepvariant" },
Expand All @@ -546,15 +548,16 @@ process{

// FREEBAYES
withName: 'MERGE_FREEBAYES' {
ext.prefix = { "${meta.id}.freebayes" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'FREEBAYES' {
//To make sure no naming conflicts ensue with module BCFTOOLS_SORT & the naming being correct in the output folder
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.freebayes" : "${meta.id}_${target_bed.simpleName}.freebayes" }
//To make sure no naming conflicts ensure with module BCFTOOLS_SORT & the naming being correct in the output folder
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}" : "${meta.id}.${target_bed.simpleName}" }
ext.args = '--min-alternate-fraction 0.1 --min-mapping-quality 1'
ext.when = { params.tools && params.tools.contains('freebayes') }
publishDir = [
Expand All @@ -563,7 +566,7 @@ process{
}

withName: 'BCFTOOLS_SORT' {
ext.prefix = { "${vcf.baseName.minus(".freebayes.vcf")}" }
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.freebayes" : "${vcf.minus("vcf")}.sort" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/" },
Expand All @@ -582,7 +585,7 @@ process{

// HAPLOTYPECALLER
withName: 'MERGE_HAPLOTYPECALLER.*' {
ext.prefix = { params.joint_germline ? "${meta.id}.g" : "${meta.id}" }
ext.prefix = { params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/haplotypecaller" },
Expand All @@ -592,7 +595,7 @@ process{

withName: 'HAPLOTYPECALLER' {
ext.args = { params.joint_germline ? "-ERC GVCF" : "" }
ext.prefix = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.g" : "${meta.id}" ) : ( params.joint_germline ? "${meta.id}_${intervals.simpleName}.g" :"${meta.id}_${intervals.simpleName}" ) }
ext.prefix = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" ) : ( params.joint_germline ? "${meta.id}.haplotypecaller.${intervals.simpleName}.g" :"${meta.id}.haplotypecaller.${intervals.simpleName}" ) }
ext.when = { params.tools && params.tools.contains('haplotypecaller') }
publishDir = [
mode: params.publish_dir_mode,
Expand All @@ -607,6 +610,7 @@ process{
]
}
withName: 'FILTERVARIANTTRANCHES' {
ext.prefix = {"${meta.id}.haplotypecaller"}
ext.args = { "--info-key CNN_1D" }
publishDir = [
mode: params.publish_dir_mode,
Expand All @@ -616,6 +620,7 @@ process{
}

withName: 'GENOTYPEGVCFS' {
ext.prefix = {"${meta.id}.haplotypecaller"}
ext.when = { params.tools && params.tools.contains('haplotypecaller') && params.joint_germline}
publishDir = [
mode: params.publish_dir_mode,
Expand All @@ -633,16 +638,16 @@ process{
]
}
withName: 'MERGE_MANTA_DIPLOID' {
ext.prefix = {"${meta.id}.diploid_sv"}
ext.prefix = {"${meta.id}.manta.diploid_sv"}
}
withName: 'MERGE_MANTA_SMALL_INDELS' {
ext.prefix = {"${meta.id}.candidate_small_indels"}
ext.prefix = {"${meta.id}.manta.candidate_small_indels"}
}
withName: 'MERGE_MANTA_SV' {
ext.prefix = {"${meta.id}.candidate_sv"}
ext.prefix = {"${meta.id}.manta.candidate_sv"}
}
withName: 'MANTA.*' {
ext.prefix = { meta.num_intervals <= 1 ? meta.id : "${meta.id}_${target_bed.simpleName}" }
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.manta" : "${meta.id}.manta.${target_bed.simpleName}" }
ext.args = { params.wes ? "--exome" : "" }
ext.when = { params.tools && params.tools.contains('manta') }
publishDir = [
Expand All @@ -662,13 +667,13 @@ process{
]
}
withName: 'MERGE_STRELKA' {
ext.prefix = {"${meta.id}.variants"}
ext.prefix = {"${meta.id}.strelka.variants"}
}
withName: 'MERGE_STRELKA_GENOME' {
ext.prefix = {"${meta.id}.genome"}
ext.prefix = {"${meta.id}.strelka.genome"}
}
withName: 'STRELKA_.*' {
ext.prefix = { meta.num_intervals <= 1 ? meta.id : "${meta.id}_${target_bed.simpleName}" }
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.strelka" : "${meta.id}.strelka.${target_bed.simpleName}" }
ext.args = { params.wes ? "--exome" : "" }
ext.when = { params.tools && params.tools.contains('strelka') }
publishDir = [
Expand All @@ -683,14 +688,15 @@ process{
withName: 'TIDDIT_SV' {
ext.when = { params.tools && params.tools.contains('tiddit') }
ext.args = { bwa_index ? "" : "--skip_assembly" }
ext.prefix = { "${meta.id}.tiddit" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" },
pattern: "*tab",
]
}
withName : 'TABIX_BGZIP_TIDDIT_SV' {
ext.prefix = { "${meta.id}.vcf" }
ext.prefix = { "${meta.id}.tiddit.vcf" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" },
Expand Down Expand Up @@ -827,20 +833,22 @@ process{

//MANTA
withName: 'MERGE_MANTA_TUMOR' {
ext.prefix = {"${meta.id}.tumor_sv"}
ext.prefix = {"${meta.id}.manta.tumor_sv"}
}

//MUTECT2
withName: 'CALCULATECONTAMINATION' {
ext.args = { "-tumor-segmentation ${meta.id}.segmentation.table" }
publishDir = [
ext.prefix = { "${meta.id}.mutect2" }
ext.args = { "-tumor-segmentation ${meta.id}.mutect2.segmentation.table" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.id}/mutect2/${filename}" }
]
}

withName: 'MERGE_MUTECT2.*' {
ext.prefix = { "${meta.id}.mutect2" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
Expand All @@ -849,7 +857,7 @@ process{
}

withName: 'FILTERMUTECTCALLS.*'{
ext.prefix = {"${meta.id}.filtered"}
ext.prefix = {"${meta.id}.mutect2.filtered"}
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/" },
Expand All @@ -858,6 +866,7 @@ process{
}

withName: 'GATHERPILEUPSUMMARIES' {
ext.prefix = { "${meta.id}.mutect2" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
Expand All @@ -866,6 +875,7 @@ process{
}

withName: 'GATHERPILEUPSUMMARIES_.*' {
ext.prefix = { "${meta.id}.mutect2" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.tumor_id}_vs_${meta.normal_id}/mutect2" },
Expand All @@ -874,7 +884,7 @@ process{
}

withName: 'GETPILEUPSUMMARIES.*' {
ext.prefix = { meta.num_intervals <= 1 ? meta.id : "${meta.id}_${intervals.simpleName}" }
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/" },
Expand All @@ -884,6 +894,7 @@ process{
}

withName: 'GETPILEUPSUMMARIES_.*' {
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/" },
Expand All @@ -893,7 +904,7 @@ process{
}

withName: 'LEARNREADORIENTATIONMODEL'{
ext.prefix = { "${meta.id}.artifactprior" }
ext.prefix = { "${meta.id}.mutect2.artifactprior" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
Expand All @@ -902,7 +913,7 @@ process{
}

withName: 'MERGEMUTECTSTATS' {
ext.prefix = { "${meta.id}" }
ext.prefix = { "${meta.id}.mutect2" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
Expand All @@ -911,7 +922,7 @@ process{
}

withName: 'MUTECT2'{
ext.prefix = { meta.num_intervals <= 1 ? meta.id : "${meta.id}_${intervals.simpleName}" }
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" }
ext.when = { params.tools && params.tools.contains('mutect2') }
ext.args = { params.ignore_soft_clipped_bases ? "--dont-use-soft-clipped-bases true --f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz" : "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz" }
publishDir = [
Expand Down Expand Up @@ -1044,7 +1055,7 @@ process{

//MANTA
withName: 'MERGE_MANTA_SOMATIC' {
ext.prefix = {"${meta.id}.somatic_sv"}
ext.prefix = {"${meta.id}.manta.somatic_sv"}
}

//MUTECT2
Expand All @@ -1067,24 +1078,25 @@ process{

//STRELKA
withName: 'MERGE_STRELKA_INDELS' {
ext.prefix = {"${meta.id}.somatic_indels"}
ext.prefix = {"${meta.id}.strelka.somatic_indels"}
}
withName: 'MERGE_STRELKA_SNVS' {
ext.prefix = {"${meta.id}.somatic_snvs"}
ext.prefix = {"${meta.id}.strelka.somatic_snvs"}
}

if (params.tools && params.tools.contains('tiddit')) {
//TIDDIT
//TIDDIT
withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV' {
ext.prefix = {"${meta.id}.normal.vcf"}
ext.prefix = {"${meta.id}.tiddit.normal.vcf"}
}

withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_TUMOR:TABIX_BGZIP_TIDDIT_SV' {
ext.prefix = {"${meta.id}.tumor.vcf"}
ext.prefix = {"${meta.id}.tiddit.tumor.vcf"}
}

//SVDB
withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:SVDB_MERGE' {
ext.prefix = { "${meta.id}.tiddit" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" },
Expand All @@ -1099,7 +1111,7 @@ process{
ext.prefix = { "${vcf.baseName.minus(".vcf")}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/bcftools" },
path: { "${params.outdir}/reports/bcftools/${meta.id}/${meta.variantcaller}/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
Expand All @@ -1109,7 +1121,7 @@ process{
ext.prefix = { "${variant_file.baseName.minus(".vcf")}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/vcftools" },
path: { "${params.outdir}/reports/vcftools/${meta.id}/${meta.variantcaller}/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
Expand Down Expand Up @@ -1207,6 +1219,5 @@ process{
// MULTIQC
withName:'MULTIQC' {
errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
ext.args = { params.multiqc_config ? "--config $multiqc_custom_config" : "" }
}
}
2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -181,7 +181,7 @@
"git_sha": "f0800157544a82ae222931764483331a81812012"
},
"multiqc": {
"git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
"git_sha": "5138acca0985ca01c38a1c4fba917d83772b1106"
},
"samblaster": {
"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
Expand Down
16 changes: 11 additions & 5 deletions modules/nf-core/modules/multiqc/main.nf
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8 changes: 8 additions & 0 deletions modules/nf-core/modules/multiqc/meta.yml
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1 change: 1 addition & 0 deletions nextflow_schema.json
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Expand Up @@ -454,6 +454,7 @@
},
"ascat_chromosomes": {
"type": "string",
"description": "Chromosomes to run ASCAT on.",
"fa_icon": "fa-solid fa-text",
"default": "c(1:22, 'X')",
"help_text": "Specify specific chromosomes to run ASCAT on, i.e 'c('21', '22')'."
Expand Down
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