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Build branch main with version main (8fe9d66)

Browse Source 
Build pipeline: viash-hub.biobox.main-vhhxn

Source commit: 8fe9d66b0c

Source message: Bcftools stats (#142)

* Initial Commit

* Adding options to config

* Update on script

* update

* Adding test 2 and 3

* Update on config and test

* adding more tests

* debugging and adding tests

* Adding last tests

* removing test_data dir

* Update CHANGELOG.md

* small changes

* small change in help file

* Requested changes

---------

Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com>
This commit is contained in:
CI
2024-09-10 14:10:14 +00:00
parent beb7940138
commit 0075a8df93
227 changed files with 8115 additions and 270 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml
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@@ -185,7 +185,7 @@ build_info:
output: "target/nextflow/bcftools/bcftools_sort"
executable: "target/nextflow/bcftools/bcftools_sort/main.nf"
viash_version: "0.9.0-RC7"
git_commit: "320d044fe45e565fbc9772640ebf6f39c5584b4a"
git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/bcftools/bcftools_sort/main.nf
View File

@@ -3042,7 +3042,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/bcftools/bcftools_sort",
"viash_version" : "0.9.0-RC7",
"git_commit" : "320d044fe45e565fbc9772640ebf6f39c5584b4a",
"git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

484
target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml Normal file
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@@ -0,0 +1,484 @@
name: "bcftools_stats"
namespace: "bcftools"
version: "main"
authors:
- name: "Theodoro Gasperin Terra Camargo"
roles:
- "author"
info:
links:
email: "theodorogtc@gmail.com"
github: "tgaspe"
linkedin: "theodoro-gasperin-terra-camargo"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Bioinformatician"
argument_groups:
- name: "Inputs"
arguments:
- type: "file"
name: "--input"
alternatives:
- "-i"
description: "Input VCF/BCF file. Maximum of two files."
info: null
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: true
multiple_sep: ";"
- name: "Outputs"
arguments:
- type: "file"
name: "--output"
alternatives:
- "-o"
description: "Output txt statistics file."
info: null
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- name: "Options"
arguments:
- type: "string"
name: "--allele_frequency_bins"
alternatives:
- "--af_bins"
description: "Allele frequency bins, a list of bin values (0.1,0.5,1).\n"
info: null
example:
- "0.1,0.5,1"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--allele_frequency_bins_file"
alternatives:
- "--af_bins_file"
description: "Same as allele_frequency_bins, but in a file.\nFormat of file is\
\ one value per line. \ne.g. \n 0.1\n 0.5\n 1\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--allele_frequency_tag"
alternatives:
- "--af_tag"
description: "Allele frequency tag to use, by default estimated from AN,AC or\
\ GT.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--first_allele_only"
alternatives:
- "--first_only"
description: "Include only 1st allele at multiallelic sites.\n"
info: null
direction: "input"
- type: "string"
name: "--collapse"
alternatives:
- "--c"
description: "Treat as identical records with <snps|indels|both|all|some|none>.\n\
See https://samtools.github.io/bcftools/bcftools.html#common_options for details.\n"
info: null
required: false
choices:
- "snps"
- "indels"
- "both"
- "all"
- "some"
- "none"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--depth"
alternatives:
- "--d"
description: "Depth distribution: min,max,bin size.\n"
info: null
example:
- "0,500,1"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--exclude"
alternatives:
- "--e"
description: "Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\
\ for details.\n"
info: null
example:
- "QUAL < 30 && DP < 10"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--exons"
alternatives:
- "--E"
description: "tab-delimited file with exons for indel frameshifts statistics.\
\ \nThe columns of the file are CHR, FROM, TO, with 1-based, inclusive, positions.\
\ \nThe file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2 -e3\
\ file.gz).\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--apply_filters"
alternatives:
- "--f"
description: "Require at least one of the listed FILTER strings (e.g. \"PASS,.\"\
).\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--fasta_reference"
alternatives:
- "--F"
description: "Faidx indexed reference sequence file to determine INDEL context.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--include"
alternatives:
- "--i"
description: "Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\
\ for details.\n"
info: null
example:
- "QUAL >= 30 && DP >= 10"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--split_by_ID"
alternatives:
- "--I"
description: "Collect stats for sites with ID separately (known vs novel).\n"
info: null
direction: "input"
- type: "string"
name: "--regions"
alternatives:
- "--r"
description: "Restrict to comma-separated list of regions. \nFollowing formats\
\ are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n"
info: null
example:
- "20:1000000-2000000"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--regions_file"
alternatives:
- "--R"
description: "Restrict to regions listed in a file. \nRegions can be specified\
\ either on a VCF, BED, or tab-delimited file (the default). \nFor more information\
\ check manual.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--regions_overlap"
description: "This option controls how overlapping records are determined: \n\
set to 'pos' or '0' if the VCF record has to have POS inside a region (this\
\ corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if\
\ also overlapping records with POS outside a region should be included (this\
\ is the default behavior of -r/-R, \nand includes indels with POS at the end\
\ of a region, which are technically outside the region); \nor set to 'variant'\
\ or '2' to include only true overlapping variation (compare the full VCF representation\
\ \"TA>T-\" vs the true sequence variation \"A>-\").\n"
info: null
required: false
choices:
- "pos"
- "record"
- "variant"
- "0"
- "1"
- "2"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--samples"
alternatives:
- "--s"
description: "List of samples for sample stats, \"-\" to include all samples.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--samples_file"
alternatives:
- "--S"
description: "File of samples to include.\ne.g. \n sample1 1\n sample2 \
\ 2\n sample3 2\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--targets"
alternatives:
- "--t"
description: "Similar as -r, --regions, but the next position is accessed by streaming\
\ the whole VCF/BCF \nrather than using the tbi/csi index. Both -r and -t options\
\ can be applied simultaneously: -r uses the \nindex to jump to a region and\
\ -t discards positions which are not in the targets. Unlike -r, targets \n\
can be prefixed with \"^\" to request logical complement. For example, \"^X,Y,MT\"\
\ indicates that \nsequences X, Y and MT should be skipped. Yet another difference\
\ between the -t/-T and -r/-R is \nthat -r/-R checks for proper overlaps and\
\ considers both POS and the end position of an indel, \nwhile -t/-T considers\
\ the POS coordinate only (by default; see also --regions-overlap and --targets-overlap).\
\ \nNote that -t cannot be used in combination with -T.\nFollowing formats are\
\ supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n"
info: null
example:
- "20:1000000-2000000"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--targets_file"
alternatives:
- "--T"
description: "Similar to --regions_file option but streams rather than index-jumps.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--targets_overlaps"
description: "Include if POS in the region (0), record overlaps (1), variant overlaps\
\ (2).\n"
info: null
required: false
choices:
- "pos"
- "record"
- "variant"
- "0"
- "1"
- "2"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--user_tstv"
alternatives:
- "--u"
description: "Collect Ts/Tv stats for any tag using the given binning [0:1:100].\n\
Format is <TAG[:min:max:n]>.\nA subfield can be selected as e.g. 'PV4[0]', here\
\ the first value of the PV4 tag.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--verbose"
alternatives:
- "--v"
description: "Produce verbose per-site and per-sample output.\n"
info: null
direction: "input"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
description: "Parses VCF or BCF and produces a txt stats file which can be plotted\
\ using plot-vcfstats.\nWhen two files are given, the program generates separate\
\ stats for intersection\nand the complements. By default only sites are compared,\
\ -s/-S must given to include\nalso sample columns.\n"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
info: null
status: "enabled"
requirements:
commands:
- "ps"
keywords:
- "Stats"
- "VCF"
- "BCF"
license: "MIT/Expat, GNU"
references:
doi:
- "https://doi.org/10.1093/gigascience/giab008"
links:
repository: "https://github.com/samtools/bcftools"
homepage: "https://samtools.github.io/bcftools/"
documentation: "https://samtools.github.io/bcftools/bcftools.html#stats"
issue_tracker: "https://github.com/samtools/bcftools/issues"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "bcftools"
- "procps"
interactive: false
- type: "docker"
run:
- "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\
\ //p')\\\"\" > /var/software_versions.txt\n"
test_setup:
- type: "apt"
packages:
- "tabix"
interactive: false
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/bcftools/bcftools_stats/config.vsh.yaml"
runner: "nextflow"
engine: "docker|native"
output: "target/nextflow/bcftools/bcftools_stats"
executable: "target/nextflow/bcftools/bcftools_stats/main.nf"
viash_version: "0.9.0-RC7"
git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"
- "sequencing"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/biobox"
issue_tracker: "https://github.com/viash-hub/biobox/issues"

3948
target/nextflow/bcftools/bcftools_stats/main.nf Normal file
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target/nextflow/bcftools/bcftools_stats/nextflow.config Normal file
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@@ -0,0 +1,126 @@
manifest {
name = 'bcftools/bcftools_stats'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'main'
description = 'Parses VCF or BCF and produces a txt stats file which can be plotted using plot-vcfstats.\nWhen two files are given, the program generates separate stats for intersection\nand the complements. By default only sites are compared, -s/-S must given to include\nalso sample columns.\n'
author = 'Theodoro Gasperin Terra Camargo'
}
process.container = 'nextflow/bash:latest'
// detect tempdir
tempDir = java.nio.file.Paths.get(
System.getenv('NXF_TEMP') ?:
System.getenv('VIASH_TEMP') ?:
System.getenv('TEMPDIR') ?:
System.getenv('TMPDIR') ?:
'/tmp'
).toAbsolutePath()
profiles {
no_publish {
process {
withName: '.*' {
publishDir = [
enabled: false
]
}
}
}
mount_temp {
docker.temp = tempDir
podman.temp = tempDir
charliecloud.temp = tempDir
}
docker {
docker.enabled = true
// docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
}
process{
withLabel: mem1gb { memory = 1000000000.B }
withLabel: mem2gb { memory = 2000000000.B }
withLabel: mem5gb { memory = 5000000000.B }
withLabel: mem10gb { memory = 10000000000.B }
withLabel: mem20gb { memory = 20000000000.B }
withLabel: mem50gb { memory = 50000000000.B }
withLabel: mem100gb { memory = 100000000000.B }
withLabel: mem200gb { memory = 200000000000.B }
withLabel: mem500gb { memory = 500000000000.B }
withLabel: mem1tb { memory = 1000000000000.B }
withLabel: mem2tb { memory = 2000000000000.B }
withLabel: mem5tb { memory = 5000000000000.B }
withLabel: mem10tb { memory = 10000000000000.B }
withLabel: mem20tb { memory = 20000000000000.B }
withLabel: mem50tb { memory = 50000000000000.B }
withLabel: mem100tb { memory = 100000000000000.B }
withLabel: mem200tb { memory = 200000000000000.B }
withLabel: mem500tb { memory = 500000000000000.B }
withLabel: mem1gib { memory = 1073741824.B }
withLabel: mem2gib { memory = 2147483648.B }
withLabel: mem4gib { memory = 4294967296.B }
withLabel: mem8gib { memory = 8589934592.B }
withLabel: mem16gib { memory = 17179869184.B }
withLabel: mem32gib { memory = 34359738368.B }
withLabel: mem64gib { memory = 68719476736.B }
withLabel: mem128gib { memory = 137438953472.B }
withLabel: mem256gib { memory = 274877906944.B }
withLabel: mem512gib { memory = 549755813888.B }
withLabel: mem1tib { memory = 1099511627776.B }
withLabel: mem2tib { memory = 2199023255552.B }
withLabel: mem4tib { memory = 4398046511104.B }
withLabel: mem8tib { memory = 8796093022208.B }
withLabel: mem16tib { memory = 17592186044416.B }
withLabel: mem32tib { memory = 35184372088832.B }
withLabel: mem64tib { memory = 70368744177664.B }
withLabel: mem128tib { memory = 140737488355328.B }
withLabel: mem256tib { memory = 281474976710656.B }
withLabel: mem512tib { memory = 562949953421312.B }
withLabel: cpu1 { cpus = 1 }
withLabel: cpu2 { cpus = 2 }
withLabel: cpu5 { cpus = 5 }
withLabel: cpu10 { cpus = 10 }
withLabel: cpu20 { cpus = 20 }
withLabel: cpu50 { cpus = 50 }
withLabel: cpu100 { cpus = 100 }
withLabel: cpu200 { cpus = 200 }
withLabel: cpu500 { cpus = 500 }
withLabel: cpu1000 { cpus = 1000 }
}

338
target/nextflow/bcftools/bcftools_stats/nextflow_schema.json Normal file
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@@ -0,0 +1,338 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "bcftools_stats",
"description": "Parses VCF or BCF and produces a txt stats file which can be plotted using plot-vcfstats.\nWhen two files are given, the program generates separate stats for intersection\nand the complements. By default only sites are compared, -s/-S must given to include\nalso sample columns.\n",
"type": "object",
"definitions": {
"inputs" : {
"title": "Inputs",
"type": "object",
"description": "No description",
"properties": {
"input": {
"type":
"string",
"description": "Type: List of `file`, required, multiple_sep: `\";\"`. Input VCF/BCF file",
"help_text": "Type: List of `file`, required, multiple_sep: `\";\"`. Input VCF/BCF file. Maximum of two files."
}
}
},
"outputs" : {
"title": "Outputs",
"type": "object",
"description": "No description",
"properties": {
"output": {
"type":
"string",
"description": "Type: `file`, required, default: `$id.$key.output.output`. Output txt statistics file",
"help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output txt statistics file."
,
"default": "$id.$key.output.output"
}
}
},
"options" : {
"title": "Options",
"type": "object",
"description": "No description",
"properties": {
"allele_frequency_bins": {
"type":
"string",
"description": "Type: `string`, example: `0.1,0.5,1`. Allele frequency bins, a list of bin values (0",
"help_text": "Type: `string`, example: `0.1,0.5,1`. Allele frequency bins, a list of bin values (0.1,0.5,1).\n"
}
,
"allele_frequency_bins_file": {
"type":
"string",
"description": "Type: `file`. Same as allele_frequency_bins, but in a file",
"help_text": "Type: `file`. Same as allele_frequency_bins, but in a file.\nFormat of file is one value per line. \ne.g. \n 0.1\n 0.5\n 1\n"
}
,
"allele_frequency_tag": {
"type":
"string",
"description": "Type: `string`. Allele frequency tag to use, by default estimated from AN,AC or GT",
"help_text": "Type: `string`. Allele frequency tag to use, by default estimated from AN,AC or GT.\n"
}
,
"first_allele_only": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Include only 1st allele at multiallelic sites",
"help_text": "Type: `boolean_true`, default: `false`. Include only 1st allele at multiallelic sites.\n"
,
"default": "False"
}
,
"collapse": {
"type":
"string",
"description": "Type: `string`, choices: ``snps`, `indels`, `both`, `all`, `some`, `none``. Treat as identical records with \u003csnps|indels|both|all|some|none\u003e",
"help_text": "Type: `string`, choices: ``snps`, `indels`, `both`, `all`, `some`, `none``. Treat as identical records with \u003csnps|indels|both|all|some|none\u003e.\nSee https://samtools.github.io/bcftools/bcftools.html#common_options for details.\n",
"enum": ["snps", "indels", "both", "all", "some", "none"]
}
,
"depth": {
"type":
"string",
"description": "Type: `string`, example: `0,500,1`. Depth distribution: min,max,bin size",
"help_text": "Type: `string`, example: `0,500,1`. Depth distribution: min,max,bin size.\n"
}
,
"exclude": {
"type":
"string",
"description": "Type: `string`, example: `QUAL \u003c 30 \u0026\u0026 DP \u003c 10`. Exclude sites for which the expression is true",
"help_text": "Type: `string`, example: `QUAL \u003c 30 \u0026\u0026 DP \u003c 10`. Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions for details.\n"
}
,
"exons": {
"type":
"string",
"description": "Type: `file`. tab-delimited file with exons for indel frameshifts statistics",
"help_text": "Type: `file`. tab-delimited file with exons for indel frameshifts statistics. \nThe columns of the file are CHR, FROM, TO, with 1-based, inclusive, positions. \nThe file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2 -e3 file.gz).\n"
}
,
"apply_filters": {
"type":
"string",
"description": "Type: `string`. Require at least one of the listed FILTER strings (e",
"help_text": "Type: `string`. Require at least one of the listed FILTER strings (e.g. \"PASS,.\").\n"
}
,
"fasta_reference": {
"type":
"string",
"description": "Type: `file`. Faidx indexed reference sequence file to determine INDEL context",
"help_text": "Type: `file`. Faidx indexed reference sequence file to determine INDEL context.\n"
}
,
"include": {
"type":
"string",
"description": "Type: `string`, example: `QUAL \u003e= 30 \u0026\u0026 DP \u003e= 10`. Select sites for which the expression is true",
"help_text": "Type: `string`, example: `QUAL \u003e= 30 \u0026\u0026 DP \u003e= 10`. Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions for details.\n"
}
,
"split_by_ID": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Collect stats for sites with ID separately (known vs novel)",
"help_text": "Type: `boolean_true`, default: `false`. Collect stats for sites with ID separately (known vs novel).\n"
,
"default": "False"
}
,
"regions": {
"type":
"string",
"description": "Type: `string`, example: `20:1000000-2000000`. Restrict to comma-separated list of regions",
"help_text": "Type: `string`, example: `20:1000000-2000000`. Restrict to comma-separated list of regions. \nFollowing formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,\u2026\u200b].\n"
}
,
"regions_file": {
"type":
"string",
"description": "Type: `file`. Restrict to regions listed in a file",
"help_text": "Type: `file`. Restrict to regions listed in a file. \nRegions can be specified either on a VCF, BED, or tab-delimited file (the default). \nFor more information check manual.\n"
}
,
"regions_overlap": {
"type":
"string",
"description": "Type: `string`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. This option controls how overlapping records are determined: \nset to \u0027pos\u0027 or \u00270\u0027 if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to \u0027record\u0027 or \u00271\u0027 if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to \u0027variant\u0027 or \u00272\u0027 to include only true overlapping variation (compare the full VCF representation \"TA\u003eT-\" vs the true sequence variation \"A\u003e-\")",
"help_text": "Type: `string`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. This option controls how overlapping records are determined: \nset to \u0027pos\u0027 or \u00270\u0027 if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to \u0027record\u0027 or \u00271\u0027 if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to \u0027variant\u0027 or \u00272\u0027 to include only true overlapping variation (compare the full VCF representation \"TA\u003eT-\" vs the true sequence variation \"A\u003e-\").\n",
"enum": ["pos", "record", "variant", "0", "1", "2"]
}
,
"samples": {
"type":
"string",
"description": "Type: `string`. List of samples for sample stats, \"-\" to include all samples",
"help_text": "Type: `string`. List of samples for sample stats, \"-\" to include all samples.\n"
}
,
"samples_file": {
"type":
"string",
"description": "Type: `file`. File of samples to include",
"help_text": "Type: `file`. File of samples to include.\ne.g. \n sample1 1\n sample2 2\n sample3 2\n"
}
,
"targets": {
"type":
"string",
"description": "Type: `string`, example: `20:1000000-2000000`. Similar as -r, --regions, but the next position is accessed by streaming the whole VCF/BCF \nrather than using the tbi/csi index",
"help_text": "Type: `string`, example: `20:1000000-2000000`. Similar as -r, --regions, but the next position is accessed by streaming the whole VCF/BCF \nrather than using the tbi/csi index. Both -r and -t options can be applied simultaneously: -r uses the \nindex to jump to a region and -t discards positions which are not in the targets. Unlike -r, targets \ncan be prefixed with \"^\" to request logical complement. For example, \"^X,Y,MT\" indicates that \nsequences X, Y and MT should be skipped. Yet another difference between the -t/-T and -r/-R is \nthat -r/-R checks for proper overlaps and considers both POS and the end position of an indel, \nwhile -t/-T considers the POS coordinate only (by default; see also --regions-overlap and --targets-overlap). \nNote that -t cannot be used in combination with -T.\nFollowing formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,\u2026\u200b].\n"
}
,
"targets_file": {
"type":
"string",
"description": "Type: `file`. Similar to --regions_file option but streams rather than index-jumps",
"help_text": "Type: `file`. Similar to --regions_file option but streams rather than index-jumps.\n"
}
,
"targets_overlaps": {
"type":
"string",
"description": "Type: `string`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. Include if POS in the region (0), record overlaps (1), variant overlaps (2)",
"help_text": "Type: `string`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. Include if POS in the region (0), record overlaps (1), variant overlaps (2).\n",
"enum": ["pos", "record", "variant", "0", "1", "2"]
}
,
"user_tstv": {
"type":
"string",
"description": "Type: `string`. Collect Ts/Tv stats for any tag using the given binning [0:1:100]",
"help_text": "Type: `string`. Collect Ts/Tv stats for any tag using the given binning [0:1:100].\nFormat is \u003cTAG[:min:max:n]\u003e.\nA subfield can be selected as e.g. \u0027PV4[0]\u0027, here the first value of the PV4 tag.\n"
}
,
"verbose": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Produce verbose per-site and per-sample output",
"help_text": "Type: `boolean_true`, default: `false`. Produce verbose per-site and per-sample output.\n"
,
"default": "False"
}
}
},
"nextflow input-output arguments" : {
"title": "Nextflow input-output arguments",
"type": "object",
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
"properties": {
"publish_dir": {
"type":
"string",
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
}
,
"param_list": {
"type":
"string",
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/inputs"
},
{
"$ref": "#/definitions/outputs"
},
{
"$ref": "#/definitions/options"
},
{
"$ref": "#/definitions/nextflow input-output arguments"
}
]
}