Skip to content

Commit

Permalink
Bump external/pipeline-Nextflow-config from 3ec7186 to f3448ac (#137
Browse files Browse the repository at this point in the history 
)

* Bump external/pipeline-Nextflow-config from `3ec7186` to `f3448ac`

Bumps [external/pipeline-Nextflow-config](https://github.com/uclahs-cds/pipeline-Nextflow-config) from `3ec7186` to `f3448ac`.
- [Release notes](https://github.com/uclahs-cds/pipeline-Nextflow-config/releases)
- [Commits](uclahs-cds/pipeline-Nextflow-config@3ec7186...f3448ac)

---
updated-dependencies:
- dependency-name: external/pipeline-Nextflow-config
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>

* Update expected test changes

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Nicholas Wiltsie <[email protected]>
  • Loading branch information
@dependabot @nwiltsie
dependabot[bot] and nwiltsie authored Mar 22, 2024
1 parent 1111cac commit c6900db
Show file tree
Hide file tree
Showing 2 changed files with 2 additions and 271 deletions.
2 changes: 1 addition & 1 deletion external/pipeline-Nextflow-config
Submodule pipeline-Nextflow-config updated 3 files
+1 −0 CHANGELOG.md
+1 −1 config/retry/retry.config
+3 −3 config/schema/schema.config
271 changes: 1 addition & 270 deletions test/configtest-F16.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -204,141 +204,6 @@
"vcftools_version": "0.1.16",
"work_dir": "/scratch/300935"
},
"params_schema": {
"dataset_id": {
"help": "Dataset identifier",
"required": true,
"type": "String"
},
"exclusion_file": {
"help": "Absolute path to an exclusion file",
"mode": "r",
"required": true,
"type": "Path"
},
"input": {
"elements": {
"BAM": {
"elements": {
"normal": {
"help": "Input BAM",
"required": true,
"type": "BAMEntryList"
},
"tumor": {
"help": "Input tumor BAM. Only to be used in exceptional use cases. Remove `normal` BAM if this is used.",
"required": false,
"type": "BAMEntryList"
}
},
"help": "Input BAM for germline SV/CNV calling",
"required": true,
"type": "InputBAMNamespace"
}
},
"help": "Input samples",
"required": true,
"type": "InputNamespace"
},
"map_qual": {
"default": "20",
"help": "Minimum Paired-End (PE) mapping quality for Delly",
"required": true,
"type": "Integer"
},
"mappability_map": {
"help": "Absolute path to a mappability file",
"mode": "r",
"required": true,
"type": "Path"
},
"merged_sites_gCNV": {
"help": "Absolute path to a BCF/VCF file containing merged gCNV sites across samples. Required when `run_regenotyping = true`.",
"mode": "r",
"required": false,
"type": "Path"
},
"merged_sites_gSV": {
"help": "Absolute path to a BCF/VCF file containing merged gSV sites across samples. Required when `run_regenotyping = true`.",
"mode": "r",
"required": false,
"type": "Path"
},
"output_dir": {
"help": "Absolute path to output directory",
"mode": "w",
"required": true,
"type": "Path"
},
"reference_fasta": {
"help": "Absolute path to a reference FASTA file",
"mode": "r",
"required": true,
"type": "Path"
},
"run_delly": {
"default": [
true
],
"help": "Run Delly",
"required": true,
"type": "Bool"
},
"run_discovery": {
"default": [
true
],
"help": "Identify SVs using Delly/Manta",
"required": true,
"type": "Bool"
},
"run_manta": {
"default": [
true
],
"help": "Run Manta",
"required": true,
"type": "Bool"
},
"run_qc": {
"default": [
true
],
"help": "Run QC",
"required": true,
"type": "Bool"
},
"run_regenotyping": {
"default": [
false
],
"help": "Regenotype SVs/CNVs using Delly",
"required": true,
"type": "Bool"
},
"save_intermediate_files": {
"default": [
false
],
"help": "Save intermediate files from the pipeline",
"required": true,
"type": "Bool"
},
"variant_type": {
"choices": [
"gSV",
"gCNV"
],
"default": [
"gSV",
"gCNV"
],
"help": "List of germline variant types to be called",
"required": true,
"type": "List"
}
},
"proc_names": "[Ljava.lang.String;@dec0ded",
"process": {
"cache": false,
"commonRetryCodes": [
Expand Down Expand Up @@ -514,140 +379,6 @@
"file": "/tmp/test-only-outputs/call-gSV-5.0.0/8675309/log-call-gSV-5.0.0-19970704T165655Z/nextflow-log/trace.txt"
},
"tz": "sun.util.calendar.ZoneInfo[id=\"UTC\",offset=0,dstSavings=0,useDaylight=false,transitions=0,lastRule=null]",
"workDir": "/scratch/300935",
"yaml": {
"dataset_id": {
"help": "Dataset identifier",
"required": true,
"type": "String"
},
"exclusion_file": {
"help": "Absolute path to an exclusion file",
"mode": "r",
"required": true,
"type": "Path"
},
"input": {
"elements": {
"BAM": {
"elements": {
"normal": {
"help": "Input BAM",
"required": true,
"type": "BAMEntryList"
},
"tumor": {
"help": "Input tumor BAM. Only to be used in exceptional use cases. Remove `normal` BAM if this is used.",
"required": false,
"type": "BAMEntryList"
}
},
"help": "Input BAM for germline SV/CNV calling",
"required": true,
"type": "InputBAMNamespace"
}
},
"help": "Input samples",
"required": true,
"type": "InputNamespace"
},
"map_qual": {
"default": "20",
"help": "Minimum Paired-End (PE) mapping quality for Delly",
"required": true,
"type": "Integer"
},
"mappability_map": {
"help": "Absolute path to a mappability file",
"mode": "r",
"required": true,
"type": "Path"
},
"merged_sites_gCNV": {
"help": "Absolute path to a BCF/VCF file containing merged gCNV sites across samples. Required when `run_regenotyping = true`.",
"mode": "r",
"required": false,
"type": "Path"
},
"merged_sites_gSV": {
"help": "Absolute path to a BCF/VCF file containing merged gSV sites across samples. Required when `run_regenotyping = true`.",
"mode": "r",
"required": false,
"type": "Path"
},
"output_dir": {
"help": "Absolute path to output directory",
"mode": "w",
"required": true,
"type": "Path"
},
"reference_fasta": {
"help": "Absolute path to a reference FASTA file",
"mode": "r",
"required": true,
"type": "Path"
},
"run_delly": {
"default": [
true
],
"help": "Run Delly",
"required": true,
"type": "Bool"
},
"run_discovery": {
"default": [
true
],
"help": "Identify SVs using Delly/Manta",
"required": true,
"type": "Bool"
},
"run_manta": {
"default": [
true
],
"help": "Run Manta",
"required": true,
"type": "Bool"
},
"run_qc": {
"default": [
true
],
"help": "Run QC",
"required": true,
"type": "Bool"
},
"run_regenotyping": {
"default": [
false
],
"help": "Regenotype SVs/CNVs using Delly",
"required": true,
"type": "Bool"
},
"save_intermediate_files": {
"default": [
false
],
"help": "Save intermediate files from the pipeline",
"required": true,
"type": "Bool"
},
"variant_type": {
"choices": [
"gSV",
"gCNV"
],
"default": [
"gSV",
"gCNV"
],
"help": "List of germline variant types to be called",
"required": true,
"type": "List"
}
}
"workDir": "/scratch/300935"
}
}

0 comments on commit c6900db

Please sign in to comment.