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Add GRIDSS somatic filter #187

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Add GRIDSS somatic filter #187

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feffc14
add pon dir param to template
Faizal-Eeman Dec 2, 2024
28d17fe
add skeleton for gridss filter with commandline updates
Faizal-Eeman Dec 2, 2024
dbd8a67
add input, output and filename formatting
Faizal-Eeman Dec 3, 2024
81cba74
include process filter_sSV_GRIDSS in main
Faizal-Eeman Dec 3, 2024
192daaa
add filter GRIDSS in F16
Faizal-Eeman Dec 3, 2024
c134335
add gridss_pon_dir to schema.yaml
Faizal-Eeman Dec 3, 2024
ab7b6e6
add filter GRIDSS to node configs
Faizal-Eeman Dec 3, 2024
df1e00b
Merge branch 'main' into mmootor-filter-gridss
nwiltsie Dec 9, 2024
cae83c3
Add new parameters to NFTest config files
nwiltsie Dec 9, 2024
2ef6d14
Update expected test output
nwiltsie Dec 9, 2024
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11 changes: 11 additions & 0 deletions config/F16.config
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,17 @@ process {
}
}

withName: filter_sSV_GRIDSS {
cpus = 1
memory = 3.GB
retry_strategy {
memory {
strategy = 'exponential'
operand = 2
}
}
}

withName: call_sSV_Delly {
cpus = 1
memory = 16.GB
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11 changes: 11 additions & 0 deletions config/F32.config
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,17 @@ process {
}
}

withName: filter_sSV_GRIDSS {
cpus = 1
memory = 6.GB
retry_strategy {
memory {
strategy = 'exponential'
operand = 2
}
}
}

withName: call_sSV_Delly {
cpus = 1
memory = 30.GB
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11 changes: 11 additions & 0 deletions config/F72.config
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,17 @@ process {
}
}

withName: filter_sSV_GRIDSS {
cpus = 1
memory = 12.GB
retry_strategy {
memory {
strategy = 'exponential'
operand = 2
}
}
}

withName: call_sSV_Delly {
cpus = 1
memory = 30.GB
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11 changes: 11 additions & 0 deletions config/M64.config
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,17 @@ process {
}
}

withName: filter_sSV_GRIDSS {
cpus = 1
memory = 20.GB
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Have you tested to see how much memory this step uses with a variety of samples. Could there be an upper bound?
Also, did you consider this:
The Hartwig Medical Foundation has reimplemented gridss_somatic_filter in Java as [GRIPSS](https://github.com/hartwigmedical/hmftools/tree/master/gripss). GRIPSS is much faster, has additional features, and is the recommended tool for somatic filtering of GRIDSS output.

retry_strategy {
memory {
strategy = 'exponential'
operand = 2
}
}
}

withName: call_sSV_Delly {
cpus = 1
memory = 120.GB
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5 changes: 5 additions & 0 deletions config/schema.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,11 @@ gridss_blacklist:
mode: 'r'
required: true
help: 'Absolute path to GRIDSS2 blacklist BED file'
gridss_pon_dir:
type: 'Path'
mode: 'r'
required: true
help: 'Absolute path to directory containing Panel Of Normals BED and BEDPE files'
exclusion_file:
type: 'Path'
mode: 'r'
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1 change: 1 addition & 0 deletions config/template.config
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ params {
// GRCh38 blacklist - /hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed
gridss_blacklist = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed"
gridss_reference_fasta = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
gridss_pon_dir = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/"
// When GRIDSS errors OutOfMemory, update `other_jvm_heap`. Default is `4.GB`
//other_jvm_heap = 4.GB

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8 changes: 7 additions & 1 deletion main.nf
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Expand Up @@ -55,7 +55,7 @@ include { call_sSV_Delly; filter_sSV_Delly } from './module/delly' addParams(
include { call_sSV_Manta } from './module/manta' addParams(
workflow_output_dir: "${params.output_dir_base}/Manta-${params.manta_version}"
)
include { preprocess_BAM_GRIDSS; run_assembly_GRIDSS; call_sSV_GRIDSS } from './module/gridss' addParams(
include { preprocess_BAM_GRIDSS; run_assembly_GRIDSS; call_sSV_GRIDSS; filter_sSV_GRIDSS } from './module/gridss' addParams(
workflow_output_dir: "${params.output_dir_base}/GRIDSS-${params.gridss_version}"
)
include { generate_sha512 as generate_sha512_BCFtools } from './module/sha512' addParams(
Expand Down Expand Up @@ -233,5 +233,11 @@ workflow {
gridss_reference_files,
params.gridss_blacklist
)

filter_sSV_GRIDSS(
params.sample,
call_sSV_GRIDSS.out.gridss_vcf,
params.gridss_pon_dir
)
}
}
42 changes: 42 additions & 0 deletions module/gridss.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -188,3 +188,45 @@ process call_sSV_GRIDSS {
${tumor_bam}
"""
}

process filter_sSV_GRIDSS {
container params.docker_image_gridss

publishDir "${params.workflow_output_dir}/output/",
pattern: "*.vcf.bgz*",
mode: "copy"

publishDir "${params.log_output_dir}/process-log",
pattern: ".command.*",
mode: "copy",
saveAs: { "${task.process.replace(':', '/')}/log${file(it).getName()}" }

input:
val(tumor_id)
path(gridss_vcf)
path(gridss_pon_dir)

output:
path "*vcf.bgz*", emit: gridss_filter_vcf_files
path ".command.*"

script:
output_filename = generate_standard_filename(
"GRIDSS2-${params.gridss_version}",
params.dataset_id,
tumor_id,
[:]
)

"""
set -euo pipefail
/usr/local/share/gridss-2.13.2-1/gridss_somatic_filter \
--pondir ${gridss_pon_dir} \
--scriptdir /usr/local/share/gridss-2.13.2-1/ \
--input ${gridss_vcf} \
--output ${output_filename}_high-confidence-somatic.vcf \
--fulloutput ${output_filename}_high-low-confidence-somatic.vcf \
--normalordinal 1 \
--tumourordinal 2
"""
}
1 change: 1 addition & 0 deletions test/config/ssv-all-tools.config
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ params {
reference_fasta = "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
gridss_reference_fasta = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
gridss_blacklist = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed"
gridss_pon_dir = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/"

exclusion_file = "/hot/resource/tool-specific-input/Delly/hg38/human.hg38.excl.tsv"

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1 change: 1 addition & 0 deletions test/config/ssv-delly.config
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ params {
reference_fasta = "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
gridss_reference_fasta = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
gridss_blacklist = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed"
gridss_pon_dir = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/"

exclusion_file = "/hot/resource/tool-specific-input/Delly/hg38/human.hg38.excl.tsv"

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1 change: 1 addition & 0 deletions test/config/ssv-manta.config
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Expand Up @@ -14,6 +14,7 @@ params {
reference_fasta = "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
gridss_reference_fasta = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
gridss_blacklist = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed"
gridss_pon_dir = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/"

exclusion_file = "/hot/resource/tool-specific-input/Delly/hg38/human.hg38.excl.tsv"

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20 changes: 20 additions & 0 deletions test/configtest-F16.json
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Expand Up @@ -72,6 +72,7 @@
"exclusion_file": "/hot/resource/tool-specific-input/Delly/hg38/human.hg38.excl.tsv",
"filter_condition": "FILTER=\\='PASS'",
"gridss_blacklist": "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed",
"gridss_pon_dir": "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/",
"gridss_reference_fasta": "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta",
"gridss_version": "2.13.2",
"input": {
Expand Down Expand Up @@ -138,6 +139,16 @@
}
}
},
"filter_sSV_GRIDSS": {
"cpus": "1",
"memory": "3 GB",
"retry_strategy": {
"memory": {
"operand": "2",
"strategy": "exponential"
}
}
},
"preprocess_BAM_GRIDSS": {
"cpus": "4",
"memory": "10 GB",
Expand Down Expand Up @@ -304,6 +315,15 @@
"closure": "retry_updater(3 GB, exponential, 2, $task.attempt, memory)"
}
},
"withName:filter_sSV_GRIDSS": {
"cpus": "1",
"memory": {
"1": "3 GB",
"2": "6 GB",
"3": "12 GB",
"closure": "retry_updater(3 GB, exponential, 2, $task.attempt, memory)"
}
},
"withName:preprocess_BAM_GRIDSS": {
"cpus": "4",
"memory": {
Expand Down
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