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e3be4c44616aec592dc33b9ad91c25bb2ec00b38
biobox/target/executable/falco/.config.vsh.yaml
CI e3be4c4461 Build branch main with version main (b0db228) 
Build pipeline: viash-hub.biobox.main-nmzjs

Source commit: b0db228825

Source message: Update readme (#177)

* update image

* add changelog

* make readme more generic

* fix url

* make images relative again
2025-05-06 20:36:16 +00:00

359 lines
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YAML
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name: "falco"
version: "main"
authors:
- name: "Toni Verbeiren"
roles:
- "author"
- "maintainer"
info:
links:
github: "tverbeiren"
linkedin: "verbeiren"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist and CEO"
argument_groups:
- name: "Input arguments"
arguments:
- type: "file"
name: "--input"
description: "input fastq files"
info: null
example:
- "input1.fastq;input2.fastq"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: true
multiple_sep: ";"
- name: "Run arguments"
arguments:
- type: "boolean_true"
name: "--nogroup"
description: "Disable grouping of bases for reads >50bp. \nAll reports will show\
\ data for every base in \nthe read. WARNING: When using this option, \nyour\
\ plots may end up a ridiculous size. You \nhave been warned!\n"
info: null
direction: "input"
- type: "file"
name: "--contaminents"
description: "Specifies a non-default file which contains \nthe list of contaminants\
\ to screen \noverrepresented sequences against. The file \nmust contain sets\
\ of named contaminants in \nthe form name[tab]sequence. Lines prefixed \nwith\
\ a hash will be ignored. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/contaminant_list.txt\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--adapters"
description: "Specifies a non-default file which contains \nthe list of adapter\
\ sequences which will be \nexplicity searched against the library. The \nfile\
\ must contain sets of named adapters in \nthe form name[tab]sequence. Lines\
\ prefixed \nwith a hash will be ignored. Default:\nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/adapter_list.txt\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--limits"
description: "Specifies a non-default file which contains \na set of criteria\
\ which will be used to \ndetermine the warn/error limits for the \nvarious\
\ modules. This file can also be used \nto selectively remove some modules from\
\ the \noutput all together. The format needs to \nmirror the default limits.txt\
\ file found in \nthe Configuration folder. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/limits.txt\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--subsample"
alternatives:
- "-s"
description: "[Falco only] makes falco faster (but \npossibly less accurate) by\
\ only processing \nreads that are a multiple of this value (using \n0-based\
\ indexing to number reads).\n"
info: null
example:
- 10
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--bisulfite"
alternatives:
- "-b"
description: "[Falco only] reads are whole genome \nbisulfite sequencing, and\
\ more Ts and fewer \nCs are therefore expected and will be \naccounted for\
\ in base content.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--reverse_complement"
alternatives:
- "-r"
description: "[Falco only] The input is a \nreverse-complement. All modules will\
\ be \ntested by swapping A/T and C/G\n"
info: null
direction: "input"
- name: "Output arguments"
arguments:
- type: "file"
name: "--outdir"
alternatives:
- "-o"
description: "Create all output files in the specified \noutput directory. FALCO-SPECIFIC:\
\ If the \ndirectory does not exists, the program will \ncreate it.\n"
info: null
example:
- "output"
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--format"
alternatives:
- "-f"
description: "Bypasses the normal sequence file format \ndetection and forces\
\ the program to use the \nspecified format. Validformats are bam, sam, \nbam_mapped,\
\ sam_mapped, fastq, fq, fastq.gz \nor fq.gz.\n"
info: null
required: false
choices:
- "bam"
- "sam"
- "bam_mapped"
- "sam_mapped"
- "fastq"
- "fq"
- "fastq.gz"
- "fq.gz"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--data_filename"
alternatives:
- "-D"
description: "[Falco only] Specify filename for FastQC \ndata output (TXT). If\
\ not specified, it will \nbe called fastq_data.txt in either the input \nfile's\
\ directory or the one specified in the \n--output flag. Only available when\
\ running \nfalco with a single input.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--report_filename"
alternatives:
- "-R"
description: "[Falco only] Specify filename for FastQC \nreport output (HTML).\
\ If not specified, it \nwill be called fastq_report.html in either \nthe input\
\ file's directory or the one \nspecified in the --output flag. Only \navailable\
\ when running falco with a single \ninput.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--summary_filename"
alternatives:
- "-S"
description: "[Falco only] Specify filename for the short \nsummary output (TXT).\
\ If not specified, it \nwill be called fastq_report.html in either \nthe input\
\ file's directory or the one \nspecified in the --output flag. Only \navailable\
\ when running falco with a single \ninput.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
description: "A C++ drop-in replacement of FastQC to assess the quality of sequence\
\ read data"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
keywords:
- "qc"
- "fastqc"
- "sequencing"
license: "GPL-3.0"
references:
doi:
- "10.12688/f1000research.21142.2"
links:
repository: "https://github.com/smithlabcode/falco"
documentation: "https://falco.readthedocs.io/en/latest/"
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:trixie-slim"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "wget"
- "build-essential"
- "g++"
- "zlib1g-dev"
- "procps"
interactive: false
- type: "docker"
run:
- "wget https://github.com/smithlabcode/falco/releases/download/v1.2.2/falco-1.2.2.tar.gz\
\ -O /tmp/falco.tar.gz && \\\ncd /tmp && \\\ntar xvf falco.tar.gz && \\\ncd\
\ falco-1.2.2 && \\\n./configure && \\\nmake all && \\\nmake install\n"
- type: "docker"
run:
- "echo \"falco: \\\"$(falco -v | sed -n 's/^falco //p')\\\"\" > /var/software_versions.txt\n"
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/falco/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/falco"
executable: "target/executable/falco/falco"
viash_version: "0.9.4"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
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"
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