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Build branch main with version main (ad89f43)

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Build pipeline: viash-hub.biobox.main-dkgvl

Source commit: ad89f43726

Source message: Add authors to package config and update author information (#180)

* Add authors to package config and update author information

* update changelog

* add linkedin
This commit is contained in:
CI
2025-06-16 10:27:22 +00:00
parent e3be4c4461
commit 93f55cc2ee
418 changed files with 55602 additions and 29307 deletions
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132
target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml
View File

@@ -371,9 +371,9 @@ build_info:
output: "target/nextflow/bbmap/bbmap_bbsplit"
executable: "target/nextflow/bbmap/bbmap_bbsplit/main.nf"
viash_version: "0.9.4"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-35-gb0db228"
git_tag: "v0.2.0-36-gad89f43"
package_config:
name: "biobox"
version: "main"
@@ -398,6 +398,134 @@ package_config:
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'main'"
authors:
- name: "Robrecht Cannoodt"
roles:
- "author"
- "maintainer"
info:
links:
email: "robrecht@data-intuitive.com"
github: "rcannood"
orcid: "0000-0003-3641-729X"
linkedin: "robrechtcannoodt"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Science Engineer"
- name: "Open Problems"
href: "https://openproblems.bio"
role: "Core Member"
- name: "Angela Oliveira Pisco"
roles:
- "author"
info:
role: "Contributor"
links:
github: "aopisco"
orcid: "0000-0003-0142-2355"
linkedin: "aopisco"
organizations:
- name: "Insitro"
href: "https://insitro.com"
role: "Director of Computational Biology"
- name: "Open Problems"
href: "https://openproblems.bio"
role: "Core Member"
- name: "Dorien Roosen"
roles:
- "author"
info:
links:
email: "dorien@data-intuitive.com"
github: "dorien-er"
linkedin: "dorien-roosen"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
- name: "Dries Schaumont"
roles:
- "author"
info:
links:
email: "dries@data-intuitive.com"
github: "DriesSchaumont"
orcid: "0000-0002-4389-0440"
linkedin: "dries-schaumont"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
- name: "Emma Rousseau"
roles:
- "author"
info:
links:
github: "emmarousseau"
linkedin: "emmarousseau1"
- name: "Jakub Majercik"
roles:
- "author"
info:
links:
email: "jakub@data-intuitive.com"
github: "jakubmajercik"
linkedin: "jakubmajercik"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Bioinformatics Engineer"
- name: "Kai Waldrant"
roles:
- "author"
info:
links:
github: "KaiWaldrant"
orcid: "0009-0003-8555-1361"
linkedin: "kaiwaldrant"
- name: "Leïla Paquay"
roles:
- "author"
info:
links:
github: "Leila011"
linkedin: "leilapaquay"
- name: "Sai Nirmayi Yasa"
roles:
- "author"
info:
links:
github: "sainirmayi"
linkedin: "sai-nirmayi-yasa"
- name: "Theodoro Gasperin Terra Camargo"
roles:
- "author"
info:
links:
email: "theodorogtc@gmail.com"
github: "tgaspe"
linkedin: "theodoro-gasperin-terra-camargo"
- name: "Toni Verbeiren"
roles:
- "author"
info:
links:
github: "tverbeiren"
linkedin: "verbeiren"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist and CEO"
- name: "Weiwei Schultz"
roles:
- "author"
info:
links:
linkedin: "weiwei-schultz"
organizations:
- name: "Janssen R&D US"
role: "Associate Director Data Sciences"
keywords:
- "bioinformatics"
- "modules"

218
target/nextflow/bbmap/bbmap_bbsplit/main.nf
View File

@@ -3450,9 +3450,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/bbmap/bbmap_bbsplit",
"viash_version" : "0.9.4",
"git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60",
"git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca",
"git_remote" : "https://github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-35-gb0db228"
"git_tag" : "v0.2.0-36-gad89f43"
},
"package_config" : {
"name" : "biobox",
@@ -3468,6 +3468,220 @@ meta = [
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"
],
"authors" : [
{
"name" : "Robrecht Cannoodt",
"roles" : [
"author",
"maintainer"
],
"info" : {
"links" : {
"email" : "robrecht@data-intuitive.com",
"github" : "rcannood",
"orcid" : "0000-0003-3641-729X",
"linkedin" : "robrechtcannoodt"
},
"organizations" : [
{
"name" : "Data Intuitive",
"href" : "https://www.data-intuitive.com",
"role" : "Data Science Engineer"
},
{
"name" : "Open Problems",
"href" : "https://openproblems.bio",
"role" : "Core Member"
}
]
}
},
{
"name" : "Angela Oliveira Pisco",
"roles" : [
"author"
],
"info" : {
"role" : "Contributor",
"links" : {
"github" : "aopisco",
"orcid" : "0000-0003-0142-2355",
"linkedin" : "aopisco"
},
"organizations" : [
{
"name" : "Insitro",
"href" : "https://insitro.com",
"role" : "Director of Computational Biology"
},
{
"name" : "Open Problems",
"href" : "https://openproblems.bio",
"role" : "Core Member"
}
]
}
},
{
"name" : "Dorien Roosen",
"roles" : [
"author"
],
"info" : {
"links" : {
"email" : "dorien@data-intuitive.com",
"github" : "dorien-er",
"linkedin" : "dorien-roosen"
},
"organizations" : [
{
"name" : "Data Intuitive",
"href" : "https://www.data-intuitive.com",
"role" : "Data Scientist"
}
]
}
},
{
"name" : "Dries Schaumont",
"roles" : [
"author"
],
"info" : {
"links" : {
"email" : "dries@data-intuitive.com",
"github" : "DriesSchaumont",
"orcid" : "0000-0002-4389-0440",
"linkedin" : "dries-schaumont"
},
"organizations" : [
{
"name" : "Data Intuitive",
"href" : "https://www.data-intuitive.com",
"role" : "Data Scientist"
}
]
}
},
{
"name" : "Emma Rousseau",
"roles" : [
"author"
],
"info" : {
"links" : {
"github" : "emmarousseau",
"linkedin" : "emmarousseau1"
}
}
},
{
"name" : "Jakub Majercik",
"roles" : [
"author"
],
"info" : {
"links" : {
"email" : "jakub@data-intuitive.com",
"github" : "jakubmajercik",
"linkedin" : "jakubmajercik"
},
"organizations" : [
{
"name" : "Data Intuitive",
"href" : "https://www.data-intuitive.com",
"role" : "Bioinformatics Engineer"
}
]
}
},
{
"name" : "Kai Waldrant",
"roles" : [
"author"
],
"info" : {
"links" : {
"github" : "KaiWaldrant",
"orcid" : "0009-0003-8555-1361",
"linkedin" : "kaiwaldrant"
}
}
},
{
"name" : "Leïla Paquay",
"roles" : [
"author"
],
"info" : {
"links" : {
"github" : "Leila011",
"linkedin" : "leilapaquay"
}
}
},
{
"name" : "Sai Nirmayi Yasa",
"roles" : [
"author"
],
"info" : {
"links" : {
"github" : "sainirmayi",
"linkedin" : "sai-nirmayi-yasa"
}
}
},
{
"name" : "Theodoro Gasperin Terra Camargo",
"roles" : [
"author"
],
"info" : {
"links" : {
"email" : "theodorogtc@gmail.com",
"github" : "tgaspe",
"linkedin" : "theodoro-gasperin-terra-camargo"
}
}
},
{
"name" : "Toni Verbeiren",
"roles" : [
"author"
],
"info" : {
"links" : {
"github" : "tverbeiren",
"linkedin" : "verbeiren"
},
"organizations" : [
{
"name" : "Data Intuitive",
"href" : "https://www.data-intuitive.com",
"role" : "Data Scientist and CEO"
}
]
}
},
{
"name" : "Weiwei Schultz",
"roles" : [
"author"
],
"info" : {
"links" : {
"linkedin" : "weiwei-schultz"
},
"organizations" : [
{
"name" : "Janssen R&D US",
"role" : "Associate Director Data Sciences"
}
]
}
}
],
"keywords" : [
"bioinformatics",
"modules",

514
target/nextflow/bbmap/bbmap_bbsplit/nextflow_schema.json
View File

@@ -1,321 +1,203 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "bbmap_bbsplit",
"description": "Split sequencing reads by mapping them to multiple references simultaneously.",
"type": "object",
"definitions": {
"input" : {
"title": "Input",
"type": "object",
"description": "No description",
"properties": {
"id": {
"type":
"string",
"description": "Type: `string`. Sample ID",
"help_text": "Type: `string`. Sample ID"
}
,
"paired": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Paired fastq files or not?",
"help_text": "Type: `boolean_true`, default: `false`. Paired fastq files or not?"
,
"default":false
}
,
"input": {
"type":
"string",
"description": "Type: List of `file`, example: `reads.fastq`, multiple_sep: `\";\"`. Input fastq files, either one or two (paired), separated by \";\"",
"help_text": "Type: List of `file`, example: `reads.fastq`, multiple_sep: `\";\"`. Input fastq files, either one or two (paired), separated by \";\"."
}
,
"ref": {
"type":
"string",
"description": "Type: List of `file`, multiple_sep: `\";\"`. Reference FASTA files, separated by \";\"",
"help_text": "Type: List of `file`, multiple_sep: `\";\"`. Reference FASTA files, separated by \";\". The primary reference should be specified first."
}
,
"only_build_index": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. If set, only builds the index",
"help_text": "Type: `boolean_true`, default: `false`. If set, only builds the index. Otherwise, mapping is performed."
,
"default":false
}
,
"build": {
"type":
"string",
"description": "Type: `file`. Index to be used for mapping",
"help_text": "Type: `file`. Index to be used for mapping. \n"
}
,
"qin": {
"type":
"string",
"description": "Type: `string`. Set to 33 or 64 to specify input quality value ASCII offset",
"help_text": "Type: `string`. Set to 33 or 64 to specify input quality value ASCII offset. Automatically detected if\nnot specified.\n"
}
,
"interleaved": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. True forces paired/interleaved input; false forces single-ended mapping",
"help_text": "Type: `boolean_true`, default: `false`. True forces paired/interleaved input; false forces single-ended mapping.\nIf not specified, interleaved status will be autodetected from read names.\n"
,
"default":false
}
,
"maxindel": {
"type":
"integer",
"description": "Type: `integer`, example: `20`. Don\u0027t look for indels longer than this",
"help_text": "Type: `integer`, example: `20`. Don\u0027t look for indels longer than this. Lower is faster. Set to \u003e=100k for RNA-seq.\n"
}
,
"minratio": {
"type":
"number",
"description": "Type: `double`, example: `0.56`. Fraction of max alignment score required to keep a site",
"help_text": "Type: `double`, example: `0.56`. Fraction of max alignment score required to keep a site. Higher is faster.\n"
}
,
"minhits": {
"type":
"integer",
"description": "Type: `integer`, example: `1`. Minimum number of seed hits required for candidate sites",
"help_text": "Type: `integer`, example: `1`. Minimum number of seed hits required for candidate sites. Higher is faster.\n"
}
,
"ambiguous": {
"type":
"string",
"description": "Type: `string`, example: `best`, choices: ``best`, `toss`, `random`, `all``. Set behavior on ambiguously-mapped reads (with multiple top-scoring mapping locations)",
"help_text": "Type: `string`, example: `best`, choices: ``best`, `toss`, `random`, `all``. Set behavior on ambiguously-mapped reads (with multiple top-scoring mapping locations).\n * best Use the first best site (Default)\n * toss Consider unmapped\n * random Select one top-scoring site randomly\n * all Retain all top-scoring sites. Does not work yet with SAM output\n",
"enum": ["best", "toss", "random", "all"]
}
,
"ambiguous2": {
"type":
"string",
"description": "Type: `string`, example: `best`, choices: ``best`, `toss`, `all`, `split``. Set behavior only for reads that map ambiguously to multiple different references",
"help_text": "Type: `string`, example: `best`, choices: ``best`, `toss`, `all`, `split``. Set behavior only for reads that map ambiguously to multiple different references.\nNormal \u0027ambiguous=\u0027 controls behavior on all ambiguous reads;\nAmbiguous2 excludes reads that map ambiguously within a single reference.\n * best Use the first best site (Default)\n * toss Consider unmapped\n * all Write a copy to the output for each reference to which it maps\n * split Write a copy to the AMBIGUOUS_ output for each reference to which it maps\n",
"enum": ["best", "toss", "all", "split"]
}
,
"qtrim": {
"type":
"string",
"description": "Type: `string`, choices: ``l`, `r`, `lr``. Quality-trim ends to Q5 before mapping",
"help_text": "Type: `string`, choices: ``l`, `r`, `lr``. Quality-trim ends to Q5 before mapping. Options are \u0027l\u0027 (left), \u0027r\u0027 (right), and \u0027lr\u0027 (both).\n",
"enum": ["l", "r", "lr"]
}
,
"untrim": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Undo trimming after mapping",
"help_text": "Type: `boolean_true`, default: `false`. Undo trimming after mapping. Untrimmed bases will be soft-clipped in cigar strings."
,
"default":false
}
}
},
"output" : {
"title": "Output",
"type": "object",
"description": "No description",
"properties": {
"index": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.index`, example: `BBSplit_index`. Location to write the index",
"help_text": "Type: `file`, default: `$id.$key.index`, example: `BBSplit_index`. Location to write the index.\n"
,
"default":"$id.$key.index"
}
,
"fastq_1": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.fastq_1.fastq`, example: `read_out1.fastq`. Output file for read 1",
"help_text": "Type: `file`, default: `$id.$key.fastq_1.fastq`, example: `read_out1.fastq`. Output file for read 1.\n"
,
"default":"$id.$key.fastq_1.fastq"
}
,
"fastq_2": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.fastq_2.fastq`, example: `read_out2.fastq`. Output file for read 2",
"help_text": "Type: `file`, default: `$id.$key.fastq_2.fastq`, example: `read_out2.fastq`. Output file for read 2.\n"
,
"default":"$id.$key.fastq_2.fastq"
}
,
"sam2bam": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.sam2bam.sh`, example: `script.sh`. Write a shell script to \u0027file\u0027 that will turn the sam output into a sorted, indexed bam file",
"help_text": "Type: `file`, default: `$id.$key.sam2bam.sh`, example: `script.sh`. Write a shell script to \u0027file\u0027 that will turn the sam output into a sorted, indexed bam file.\n"
,
"default":"$id.$key.sam2bam.sh"
}
,
"scafstats": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.scafstats.txt`, example: `scaffold_stats.txt`. Write statistics on how many reads mapped to which scaffold to this file",
"help_text": "Type: `file`, default: `$id.$key.scafstats.txt`, example: `scaffold_stats.txt`. Write statistics on how many reads mapped to which scaffold to this file.\n"
,
"default":"$id.$key.scafstats.txt"
}
,
"refstats": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.refstats.txt`, example: `reference_stats.txt`. Write statistics on how many reads were assigned to which reference to this file",
"help_text": "Type: `file`, default: `$id.$key.refstats.txt`, example: `reference_stats.txt`. Write statistics on how many reads were assigned to which reference to this file.\nUnmapped reads whose mate mapped to a reference are considered assigned and will be counted.\n"
,
"default":"$id.$key.refstats.txt"
}
,
"nzo": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Only print lines with nonzero coverage",
"help_text": "Type: `boolean_true`, default: `false`. Only print lines with nonzero coverage."
,
"default":false
}
,
"bbmap_args": {
"type":
"string",
"description": "Type: `string`. Additional arguments from BBMap to pass to BBSplit",
"help_text": "Type: `string`. Additional arguments from BBMap to pass to BBSplit.\n"
}
}
},
"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/input"
"$schema": "https://json-schema.org/draft/2020-12/schema",
"title": "bbmap_bbsplit",
"description": "Split sequencing reads by mapping them to multiple references simultaneously.",
"type": "object",
"$defs": {
"input": {
"title": "Input",
"type": "object",
"description": "No description",
"properties": {
"id": {
"type": "string",
"description": "Sample ID",
"help_text": "Type: `string`, multiple: `False`. "
},
"paired": {
"type": "boolean",
"description": "Paired fastq files or not?",
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
"default": false
},
"input": {
"type": "array",
"items": {
"type": "string"
},
"format": "path",
"description": "Input fastq files, either one or two (paired), separated by \";\".",
"help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"reads.fastq\"]`. "
},
"ref": {
"type": "array",
"items": {
"type": "string"
},
"format": "path",
"description": "Reference FASTA files, separated by \";\"",
"help_text": "Type: `file`, multiple: `True`, direction: `input`. "
},
"only_build_index": {
"type": "boolean",
"description": "If set, only builds the index",
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
"default": false
},
"build": {
"type": "string",
"format": "path",
"description": "Index to be used for mapping",
"help_text": "Type: `file`, multiple: `False`, direction: `input`. "
},
"qin": {
"type": "string",
"description": "Set to 33 or 64 to specify input quality value ASCII offset",
"help_text": "Type: `string`, multiple: `False`. "
},
"interleaved": {
"type": "boolean",
"description": "True forces paired/interleaved input; false forces single-ended mapping.\nIf not specified, interleaved status will be autodetected from read names.\n",
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
"default": false
},
"maxindel": {
"type": "integer",
"description": "Don't look for indels longer than this",
"help_text": "Type: `integer`, multiple: `False`, example: `20`. "
},
"minratio": {
"type": "number",
"description": "Fraction of max alignment score required to keep a site",
"help_text": "Type: `double`, multiple: `False`, example: `0.56`. "
},
"minhits": {
"type": "integer",
"description": "Minimum number of seed hits required for candidate sites",
"help_text": "Type: `integer`, multiple: `False`, example: `1`. "
},
"ambiguous": {
"type": "string",
"description": "Set behavior on ambiguously-mapped reads (with multiple top-scoring mapping locations).\n * best Use the first best site (Default)\n * toss Consider unmapped\n * random Select one top-scoring site randomly\n * all Retain all top-scoring sites",
"help_text": "Type: `string`, multiple: `False`, example: `\"best\"`, choices: ``best`, `toss`, `random`, `all``. ",
"enum": [
"best",
"toss",
"random",
"all"
]
},
"ambiguous2": {
"type": "string",
"description": "Set behavior only for reads that map ambiguously to multiple different references.\nNormal 'ambiguous=' controls behavior on all ambiguous reads;\nAmbiguous2 excludes reads that map ambiguously within a single reference.\n * best Use the first best site (Default)\n * toss Consider unmapped\n * all Write a copy to the output for each reference to which it maps\n * split Write a copy to the AMBIGUOUS_ output for each reference to which it maps\n",
"help_text": "Type: `string`, multiple: `False`, example: `\"best\"`, choices: ``best`, `toss`, `all`, `split``. ",
"enum": [
"best",
"toss",
"all",
"split"
]
},
"qtrim": {
"type": "string",
"description": "Quality-trim ends to Q5 before mapping",
"help_text": "Type: `string`, multiple: `False`, choices: ``l`, `r`, `lr``. ",
"enum": [
"l",
"r",
"lr"
]
},
"untrim": {
"type": "boolean",
"description": "Undo trimming after mapping",
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
"default": false
}
}
},
{
"$ref": "#/definitions/output"
"output": {
"title": "Output",
"type": "object",
"description": "No description",
"properties": {
"index": {
"type": "string",
"format": "path",
"description": "Location to write the index.\n",
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.index\"`, direction: `output`, example: `\"BBSplit_index\"`. ",
"default": "$id.$key.index"
},
"fastq_1": {
"type": "string",
"format": "path",
"description": "Output file for read 1.\n",
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.fastq_1.fastq\"`, direction: `output`, example: `\"read_out1.fastq\"`. ",
"default": "$id.$key.fastq_1.fastq"
},
"fastq_2": {
"type": "string",
"format": "path",
"description": "Output file for read 2.\n",
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.fastq_2.fastq\"`, direction: `output`, example: `\"read_out2.fastq\"`. ",
"default": "$id.$key.fastq_2.fastq"
},
"sam2bam": {
"type": "string",
"format": "path",
"description": "Write a shell script to 'file' that will turn the sam output into a sorted, indexed bam file.\n",
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.sam2bam.sh\"`, direction: `output`, example: `\"script.sh\"`. ",
"default": "$id.$key.sam2bam.sh"
},
"scafstats": {
"type": "string",
"format": "path",
"description": "Write statistics on how many reads mapped to which scaffold to this file.\n",
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.scafstats.txt\"`, direction: `output`, example: `\"scaffold_stats.txt\"`. ",
"default": "$id.$key.scafstats.txt"
},
"refstats": {
"type": "string",
"format": "path",
"description": "Write statistics on how many reads were assigned to which reference to this file.\nUnmapped reads whose mate mapped to a reference are considered assigned and will be counted.\n",
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.refstats.txt\"`, direction: `output`, example: `\"reference_stats.txt\"`. ",
"default": "$id.$key.refstats.txt"
},
"nzo": {
"type": "boolean",
"description": "Only print lines with nonzero coverage.",
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
"default": false
},
"bbmap_args": {
"type": "string",
"description": "Additional arguments from BBMap to pass to BBSplit.\n",
"help_text": "Type: `string`, multiple: `False`. "
}
}
},
{
"$ref": "#/definitions/nextflow input-output arguments"
"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": "Path to an output directory.",
"help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
}
}
}
]
},
"allOf": [
{
"$ref": "#/$defs/input"
},
{
"$ref": "#/$defs/output"
},
{
"$ref": "#/$defs/nextflow input-output arguments"
}
]
}