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Gatkcnvcaller #362
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ramprasadn
merged 48 commits into
nf-core:dev
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genomic-medicine-sweden:gatkcnvcaller
Jul 7, 2023
Merged
Gatkcnvcaller #362
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e9cfd84
Add Gatk4 GermlineCNVCaller module
ryanjameskennedy fe10e4e
Merge branch 'dev' into add-gatk4-germlinecnvcaller
ryanjameskennedy 120a674
GATK nightly bug fix
ryanjameskennedy edca36c
Merge dev changes into add-gatk4-germlinecnvcaller
ryanjameskennedy d8c7be8
Merge branch 'nf-core:dev' into add-gatk4-germlinecnvcaller
ryanjameskennedy 58d65ba
Install nf-core modules
ryanjameskennedy 02eaa84
Update and add configs
ryanjameskennedy 349fc83
Update and add subworkflows
ryanjameskennedy 85b6825
Update workflow
ryanjameskennedy d1a8b8e
Install & update modules
ryanjameskennedy a5d6de2
Fix formatting and structure
ryanjameskennedy 5be1daa
Fix linting error
ryanjameskennedy 3e20057
Update test_one_sample.config
ryanjameskennedy d18d4cd
Add gatk params to rd main.nf
ryanjameskennedy 6083b1b
Add meta to blacklist bed
ryanjameskennedy d0e8820
Change germlinecnvcaller input channel
ryanjameskennedy 343f62f
Update nextflow_schema.json
ryanjameskennedy 34f1a25
Fix prettier linting error
ryanjameskennedy 9a24dda
Update configs re hg38.blacklist_interval.bed
ryanjameskennedy f8e9910
Fix channel errors
ryanjameskennedy 57a0dbe
Remove cohort modules
ryanjameskennedy 710d910
Fix pipeline test errors
ryanjameskennedy 77f0e9f
Minor test changes
ryanjameskennedy 53bd239
Merge branch 'dev' of github.com:nf-core/raredisease into gatkcnvcaller
ramprasadn cf979be
Merge branch 'master' of github.com:nf-core/raredisease into gatkcnvc…
ramprasadn 95bb1b3
fix changes
ramprasadn 4b398cb
Merge branch 'devplaceholder' of github.com:nf-core/raredisease into …
ramprasadn a9d1423
Merge branch 'dev' of github.com:nf-core/raredisease into gatkcnvcaller
ramprasadn 3ece075
Merge branch 'dev' of github.com:nf-core/raredisease into gatkcnvcaller
ramprasadn 3bff114
update preprocessintervals
ramprasadn b91c958
update modules
ramprasadn f5a263d
Merge branch 'gatkcnvcaller' of github.com:genomic-medicine-sweden/ra…
ramprasadn 552eb0c
Merge branch 'dev' of github.com:nf-core/raredisease into gatkcnvcaller
ramprasadn 22135b0
rename params
ramprasadn 494cfea
rename channels
ramprasadn d93c45b
update subworkflow
ramprasadn 12d6302
prettier
ramprasadn bafc512
remove modules [skip ci]
ramprasadn 20c4f0d
Merge branch 'gatkcnvcaller' of github.com:genomic-medicine-sweden/ra…
ramprasadn d2d019c
Merge branch 'dev' of github.com:nf-core/raredisease into gatkcnvcaller
ramprasadn 3665ff3
update docs
ramprasadn 6f589bb
update usage
ramprasadn e39caf5
update sample
ramprasadn d08a95f
format usage
ramprasadn 14f8869
remove hidden
ramprasadn 66efabc
review suggestions
ramprasadn 2f83bbb
Merge branch 'dev' of github.com:nf-core/raredisease into gatkcnvcaller
ramprasadn 007c5ee
Merge branch 'dev' into gatkcnvcaller
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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,39 @@ | ||
/* | ||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
Config file for defining DSL2 per module options and publishing paths | ||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
Available keys to override module options: | ||
ext.args = Additional arguments appended to command in module. | ||
ext.args2 = Second set of arguments appended to command in module (multi-tool modules). | ||
ext.args3 = Third set of arguments appended to command in module (multi-tool modules). | ||
ext.prefix = File name prefix for output files. | ||
ext.when = Conditional clause | ||
---------------------------------------------------------------------------------------- | ||
*/ | ||
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// | ||
// gcnvcaller calling options | ||
// | ||
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process { | ||
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withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_GERMLINECNVCALLER.*" { | ||
publishDir = [ | ||
enabled: false | ||
] | ||
ext.when = !params.skip_cnv_calling | ||
} | ||
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withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_GERMLINECNVCALLER:GATK4_COLLECTREADCOUNTS" { | ||
ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY" | ||
} | ||
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withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_GERMLINECNVCALLER:GATK4_DETERMINEGERMLINECONTIGPLOIDY" { | ||
ext.prefix = { "${meta.id}_ploidy" } | ||
} | ||
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withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_GERMLINECNVCALLER:GATK4_GERMLINECNVCALLER" { | ||
ext.args = "--run-mode CASE" | ||
ext.prefix = { "${meta.id}_${model.simpleName}" } | ||
} | ||
} |
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Original file line number | Diff line number | Diff line change | ||||
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@@ -117,4 +117,15 @@ process { | |||||
enabled: false | ||||||
] | ||||||
} | ||||||
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withName: '.*PREPARE_REFERENCES:GATK_PREPROCESS_WGS' { | ||||||
ext.args = { "--padding 0 --interval-merging-rule OVERLAPPING_ONLY --exclude-intervals ${params.mito_name}" } | ||||||
ext.when = { params.analysis_type.equals("wgs") && !params.readcount_intervals } | ||||||
} | ||||||
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withName: '.*PREPARE_REFERENCES:GATK_PREPROCESS_WES' { | ||||||
ext.args = { "--bin-length 0 --interval-merging-rule OVERLAPPING_ONLY --exclude-intervals ${params.mito_name}" } | ||||||
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Suggested change
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ext.when = { params.analysis_type.equals("wes") && !params.readcount_intervals } | ||||||
} | ||||||
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} |
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Original file line number | Diff line number | Diff line change | ||
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@@ -10,6 +10,8 @@ The directories listed below will be created in the results directory after the | |||
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The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: | ||||
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#### GATK GermlineCNVCaller (CNV calling) | ||||
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Suggested change
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- [Alignment](#alignment) | ||||
- [Mapping](#mapping) | ||||
- [Bwa-mem2](#bwa-mem2) | ||||
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@@ -33,6 +35,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d | |||
- [Variant calling - SV](#variant-calling---sv) | ||||
- [Manta](#manta) | ||||
- [TIDDIT sv](#tiddit-sv) | ||||
- [GATK GermlineCNVCaller - CNV calling](#gatk-germlinecnvcaller---cnv-calling) | ||||
- [SVDB merge](#svdb-merge) | ||||
- [Variant calling - repeat expansions](#variant-calling---repeat-expansions) | ||||
- [Expansion Hunter](#expansion-hunter) | ||||
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@@ -252,9 +255,13 @@ The pipeline performs variant calling using [Sentieon DNAscope](https://support. | |||
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[TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT) is used to identify chromosomal rearrangements using sequencing data. TIDDIT identifies intra and inter-chromosomal translocations, deletions, tandem-duplications and inversions, using supplementary alignments as well as discordant pairs. TIDDIT searches for discordant reads and split reads (supplementary alignments). Output vcf files are treated as intermediates and are not placed in the output folder by default. | ||||
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#### GATK GermlineCNVCaller - CNV calling | ||||
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[GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk) is used to identify copy number variants in germline samples given their read counts and a model describing a sample's ploidy. Output vcf files are treated as intermediates and are not placed in the output folder by default. | ||||
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#### SVDB merge | ||||
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[SVDB merge](https://github.com/J35P312/SVDB#merge) is used to merge the variant calls from both 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_cnv_calling is set to false), Manta, and TIDDIT. Output files are published in the output folder. | ||||
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<details markdown="1"> | ||||
<summary>Output files</summary> | ||||
|
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