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e3be4c44616aec592dc33b9ad91c25bb2ec00b38
biobox/target/executable/fastqc/.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

382 lines
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YAML
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name: "fastqc"
version: "main"
authors:
- name: "Theodoro Gasperin Terra Camargo"
roles:
- "author"
- "maintainer"
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"
description: "FASTQ file(s) to be analyzed.\n"
info: null
example:
- "input.fq"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: true
multiple_sep: ";"
- name: "Outputs"
description: "At least one of the output options (--html, --zip, --summary, --data)\
\ must be used.\n"
arguments:
- type: "file"
name: "--html"
description: "Create the HTML report of the results. \n'*' wild card must be provided\
\ in the output file name. \nWild card will be replaced by the input file basename.\n\
e.g. \n --input \"sample_1.fq\"\n --html \"*.html\"\n would create an output\
\ html file named sample_1.html\n"
info: null
example:
- "*.html"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: true
multiple_sep: ";"
- type: "file"
name: "--zip"
description: "Create the zip file(s) containing: html report, data, images, icons,\
\ summary, etc.\n'*' wild card must be provided in the output file name.\nWild\
\ card will be replaced by the input basename.\ne.g. \n --input \"sample_1.fq\"\
\n --html \"*.zip\"\n would create an output zip file named sample_1.zip\n"
info: null
example:
- "*.zip"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: true
multiple_sep: ";"
- type: "file"
name: "--summary"
description: "Create the summary file(s).\n'*' wild card must be provided in the\
\ output file name.\nWild card will be replaced by the input basename.\ne.g.\
\ \n --input \"sample_1.fq\"\n --summary \"*_summary.txt\"\n would create\
\ an output summary.txt file named sample_1_summary.txt\n"
info: null
example:
- "*_summary.txt"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: true
multiple_sep: ";"
- type: "file"
name: "--data"
description: "Create the data file(s).\n'*' wild card must be provided in the\
\ output file name.\nWild card will be replaced by the input basename.\ne.g.\
\ \n --input \"sample_1.fq\"\n --summary \"*_data.txt\"\n would create an\
\ output data.txt file named sample_1_data.txt\n"
info: null
example:
- "*_data.txt"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: true
multiple_sep: ";"
- name: "Options"
arguments:
- type: "boolean_true"
name: "--casava"
description: "Files come from raw casava output. Files in the same sample\ngroup\
\ (differing only by the group number) will be analysed\nas a set rather than\
\ individually. Sequences with the filter\nflag set in the header will be excluded\
\ from the analysis.\nFiles must have the same names given to them by casava\n\
(including being gzipped and ending with .gz) otherwise they\nwon't be grouped\
\ together correctly.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--nano"
description: "Files come from nanopore sequences and are in fast5 format. In\n\
this mode you can pass in directories to process and the program\nwill take\
\ in all fast5 files within those directories and produce\na single output file\
\ from the sequences found in all files.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--nofilter"
description: "If running with --casava then don't remove read flagged by\ncasava\
\ as poor quality when performing the QC analysis.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--nogroup"
description: "Disable grouping of bases for reads >50bp. \nAll reports will show\
\ data for every base in the read. \nWARNING: Using this option will cause fastqc\
\ to crash \nand burn if you use it on really long reads, and your \nplots may\
\ end up a ridiculous size. You have been warned!\n"
info: null
direction: "input"
- type: "integer"
name: "--min_length"
description: "Sets an artificial lower limit on the length of the \nsequence to\
\ be shown in the report. As long as you \nset this to a value greater or equal\
\ to your longest \nread length then this will be the sequence length used \n\
to create your read groups. This can be useful for making\ndirectly comparable\
\ statistics from datasets with somewhat \nvariable read lengths.\n"
info: null
example:
- 0
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--format"
alternatives:
- "-f"
description: "Bypasses the normal sequence file format detection and \nforces\
\ the program to use the specified format. \nValid formats are bam, sam, bam_mapped,\
\ sam_mapped, and fastq.\n"
info: null
example:
- "bam"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--contaminants"
alternatives:
- "-c"
description: "Specifies a non-default file which contains the list \nof contaminants\
\ to screen overrepresented sequences against. \nThe file must contain sets\
\ of named contaminants in the form\nname[tab]sequence. Lines prefixed with\
\ a hash will be ignored.\n"
info: null
example:
- "contaminants.txt"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--adapters"
alternatives:
- "-a"
description: "Specifies a non-default file which contains the list of \nadapter\
\ sequences which will be explicitly searched against \nthe library. The file\
\ must contain sets of named adapters \nin the form name[tab]sequence. Lines\
\ prefixed with a hash will be ignored.\n"
info: null
example:
- "adapters.txt"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--limits"
alternatives:
- "-l"
description: "Specifies a non-default file which contains \na set of criteria\
\ which will be used to determine \nthe warn/error limits for the various modules.\
\ \nThis file can also be used to selectively remove \nsome modules from the\
\ output altogether. The format \nneeds to mirror the default limits.txt file\
\ found in \nthe Configuration folder.\n"
info: null
example:
- "limits.txt"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--kmers"
alternatives:
- "-k"
description: "Specifies the length of Kmer to look for in the Kmer \ncontent module.\
\ Specified Kmer length must be between \n2 and 10. Default length is 7 if not\
\ specified.\n"
info: null
example:
- 7
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--quiet"
alternatives:
- "-q"
description: "Suppress all progress messages on stdout and only report errors.\n"
info: null
direction: "input"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
description: "FastQC - A high throughput sequence QC analysis tool."
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
keywords:
- "Quality control"
- "BAM"
- "SAM"
- "FASTQ"
license: "GPL-3.0, Apache-2.0"
links:
repository: "https://github.com/s-andrews/FastQC"
homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
documentation: "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/"
issue_tracker: "https://github.com/s-andrews/FastQC/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: "biocontainers/fastqc:v0.11.9_cv8"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
run:
- "echo \"fastqc: $(fastqc --version | sed -n 's/^FastQC //p')\" > /var/software_versions.txt\n"
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/fastqc/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/fastqc"
executable: "target/executable/fastqc/fastqc"
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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