CI
6f2f840fd9
Build pipeline: viash-hub.biobox.main-zp6tq
Source commit: 7f8bcc2b3e
Source message: BD rhapsody sequence analysis (#96)
* wip
* fix test
* add help
* update 2.2 args
* fix bug
* extend test data
* output separate files
* analyse missing args
* tweaks to test
* fix script
* fix test
* fix test
* move small reference
* wip generate wta test data
* don't forget about umi in r1
* remove unneeded pkg
* load reference in memory just once
* fix random choices
* extend test
* add abc immunediscoverypanel
* wip abc testing code
* fix abc test; need unique instrument, run and flowcell ids for each sample
* add smk data
* add entry to changelog
* remove old test file
* adapt test for missing read
* update description
* add comment
* ensure cwl files are absolute
* Apply suggestions from code review
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
* fix suggestion
* newer pipelines have docker requirements as a hint instead of a strict requirement
* rename str to content
* remove deleted resources
* fix containers
* fix script
* fix suggestion
* fix suggestion...
* fix test
* fix component name
* fix test
* apply suggestions
* fix test
* added note
* fix changelog
* fix changelog again
* splitting hairs here
---------
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
451 lines
14 KiB
YAML
451 lines
14 KiB
YAML
name: "busco_run"
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namespace: "busco"
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version: "main"
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authors:
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- name: "Dorien Roosen"
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roles:
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- "author"
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- "maintainer"
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info:
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links:
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email: "dorien@data-intuitive.com"
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github: "dorien-er"
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linkedin: "dorien-roosen"
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organizations:
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- name: "Data Intuitive"
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href: "https://www.data-intuitive.com"
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role: "Data Scientist"
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argument_groups:
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- name: "Inputs"
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arguments:
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- type: "file"
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name: "--input"
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alternatives:
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- "-i"
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description: "Input sequence file in FASTA format. Can be an assembled genome\
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\ or transcriptome (DNA), or protein sequences from an annotated gene set. Also\
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\ possible to use a path to a directory containing multiple input files.\n"
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info: null
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example:
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- "file.fasta"
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must_exist: true
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create_parent: true
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required: true
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--mode"
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alternatives:
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- "-m"
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description: "Specify which BUSCO analysis mode to run. There are three valid\
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\ modes:\n - geno or genome, for genome assemblies (DNA)\n - tran or transcriptome,\
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\ for transcriptome assemblies (DNA)\n - prot or proteins, for annotated gene\
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\ sets (protein)\n"
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info: null
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example:
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- "proteins"
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required: true
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choices:
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- "genome"
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- "geno"
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- "transcriptome"
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- "tran"
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- "proteins"
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- "prot"
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--lineage_dataset"
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alternatives:
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- "-l"
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description: "Specify a BUSCO lineage dataset that is most closely related to\
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\ the assembly or gene set being assessed. \nThe full list of available datasets\
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\ can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/) or by\
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\ running the busco/busco_list_datasets component.\nWhen unsure, the \"--auto_lineage\"\
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\ flag can be set to automatically find the optimal lineage path.\nBUSCO will\
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\ automatically download the requested dataset if it is not already present\
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\ in the download folder. \nYou can optionally provide a path to a local dataset\
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\ instead of a name, e.g. path/to/dataset.\nDatasets can be downloaded using\
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\ the busco/busco_download_dataset component.\n"
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info: null
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example:
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- "stramenopiles_odb10"
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- name: "Outputs"
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arguments:
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- type: "file"
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name: "--short_summary_json"
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description: "Output file for short summary in JSON format.\n"
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info: null
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example:
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- "short_summary.json"
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must_exist: true
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create_parent: true
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required: false
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direction: "output"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--short_summary_txt"
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description: "Output file for short summary in TXT format.\n"
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info: null
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example:
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- "short_summary.txt"
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must_exist: true
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create_parent: true
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required: false
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direction: "output"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--full_table"
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description: "Full table output in TSV format.\n"
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info: null
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example:
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- "full_table.tsv"
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must_exist: true
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create_parent: true
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required: false
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direction: "output"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--missing_busco_list"
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description: "Missing list output in TSV format.\n"
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info: null
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example:
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- "missing_busco_list.tsv"
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must_exist: true
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create_parent: true
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required: false
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direction: "output"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--output_dir"
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description: "The full output directory, if so desired.\n"
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info: null
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example:
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- "output_dir"
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must_exist: true
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create_parent: true
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required: false
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direction: "output"
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multiple: false
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multiple_sep: ";"
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- name: "Resource and Run Settings"
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arguments:
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- type: "boolean_true"
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name: "--force"
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description: "Force rewriting of existing files. Must be used when output files\
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\ with the provided name already exist.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--quiet"
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alternatives:
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- "-q"
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description: "Disable the info logs, displays only errors.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--restart"
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alternatives:
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- "-r"
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description: "Continue a run that had already partially completed. Restarting\
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\ skips calls to tools that have completed but performs all pre- and post-processing\
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\ steps.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--tar"
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description: "Compress some subdirectories with many files to save space.\n"
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info: null
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direction: "input"
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- name: "Lineage Dataset Settings"
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arguments:
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- type: "boolean_true"
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name: "--auto_lineage"
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description: "Run auto-lineage pipelilne to automatically determine BUSCO lineage\
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\ dataset that is most closely related to the assembly or gene set being assessed.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--auto_lineage_euk"
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description: "Run auto-placement just on eukaryota tree to find optimal lineage\
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\ path.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--auto_lineage_prok"
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description: "Run auto_lineage just on prokaryota trees to find optimum lineage\
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\ path.\n"
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info: null
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direction: "input"
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- type: "string"
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name: "--datasets_version"
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description: "Specify the version of BUSCO datasets\n"
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info: null
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example:
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- "odb10"
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- name: "Augustus Settings"
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arguments:
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- type: "boolean_true"
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name: "--augustus"
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description: "Use augustus gene predictor for eukaryote runs.\n"
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info: null
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direction: "input"
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- type: "string"
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name: "--augustus_parameters"
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description: "Additional parameters to be passed to Augustus (see Augustus documentation:\
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\ https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md).\n\
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Parameters should be contained within a single string, without whitespace and\
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\ seperated by commas.\n"
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info: null
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example:
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- "--PARAM1=VALUE1,--PARAM2=VALUE2"
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--augustus_species"
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description: "Specify the augustus species\n"
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "boolean_true"
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name: "--long"
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description: "Optimize Augustus self-training mode. This adds considerably to\
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\ the run time, but can improve results for some non-model organisms.\n"
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info: null
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direction: "input"
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- name: "BBTools Settings"
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arguments:
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- type: "integer"
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name: "--contig_break"
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description: "Number of contiguous Ns to signify a break between contigs in BBTools\
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\ analysis.\n"
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "integer"
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name: "--limit"
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description: "Number of candidate regions (contig or transcript) from the BLAST\
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\ output to consider per BUSCO.\nThis option is only effective in pipelines\
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\ using BLAST, i.e. the genome pipeline (see --augustus) or the prokaryota transcriptome\
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\ pipeline.\n"
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "boolean_true"
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name: "--scaffold_composition"
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description: "Writes ACGTN content per scaffold to a file scaffold_composition.txt.\n"
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info: null
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direction: "input"
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- name: "BLAST Settings"
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arguments:
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- type: "double"
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name: "--e_value"
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description: "E-value cutoff for BLAST searches.\n"
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- name: "Protein Gene Prediction settings"
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arguments:
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- type: "boolean_true"
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name: "--miniprot"
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description: "Use Miniprot gene predictor.\n"
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info: null
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direction: "input"
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- name: "MetaEuk Settings"
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arguments:
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- type: "boolean_true"
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name: "--metaeuk"
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description: "Use Metaeuk gene predictor.\n"
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info: null
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direction: "input"
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- type: "string"
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name: "--metaeuk_parameters"
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description: "Pass additional arguments to Metaeuk for the first run (see Metaeuk\
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\ documentation https://github.com/soedinglab/metaeuk).\nAll parameters should\
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\ be contained within a single string with no white space, with each parameter\
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\ separated by a comma.\n"
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info: null
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example:
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- "--max-overlap=15,--min-exon-aa=15"
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--metaeuk_rerun_parameters"
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description: "Pass additional arguments to Metaeuk for the second run (see Metaeuk\
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\ documentation https://github.com/soedinglab/metaeuk).\nAll parameters should\
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\ be contained within a single string with no white space, with each parameter\
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\ separated by a comma.\n"
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info: null
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example:
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- "--max-overlap=15,--min-exon-aa=15"
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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resources:
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- type: "bash_script"
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path: "script.sh"
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is_executable: true
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description: "Assessment of genome assembly and annotation completeness with single\
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\ copy orthologs"
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test_resources:
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- type: "bash_script"
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path: "test.sh"
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is_executable: true
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- type: "file"
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path: "test_data"
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info: null
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status: "enabled"
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requirements:
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commands:
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- "ps"
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keywords:
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- "Genome assembly"
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- "quality control"
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license: "MIT"
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references:
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doi:
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- "10.1007/978-1-4939-9173-0_14"
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links:
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repository: "https://gitlab.com/ezlab/busco"
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homepage: "https://busco.ezlab.org/"
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documentation: "https://busco.ezlab.org/busco_userguide.html"
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runners:
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- type: "executable"
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id: "executable"
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docker_setup_strategy: "ifneedbepullelsecachedbuild"
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- type: "nextflow"
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id: "nextflow"
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directives:
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tag: "$id"
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auto:
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simplifyInput: true
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simplifyOutput: false
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transcript: false
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publish: false
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config:
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labels:
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mem1gb: "memory = 1000000000.B"
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mem2gb: "memory = 2000000000.B"
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mem5gb: "memory = 5000000000.B"
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mem10gb: "memory = 10000000000.B"
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mem20gb: "memory = 20000000000.B"
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mem50gb: "memory = 50000000000.B"
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mem100gb: "memory = 100000000000.B"
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mem200gb: "memory = 200000000000.B"
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mem500gb: "memory = 500000000000.B"
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mem1tb: "memory = 1000000000000.B"
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mem2tb: "memory = 2000000000000.B"
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mem5tb: "memory = 5000000000000.B"
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mem10tb: "memory = 10000000000000.B"
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mem20tb: "memory = 20000000000000.B"
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mem50tb: "memory = 50000000000000.B"
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mem100tb: "memory = 100000000000000.B"
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mem200tb: "memory = 200000000000000.B"
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mem500tb: "memory = 500000000000000.B"
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mem1gib: "memory = 1073741824.B"
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mem2gib: "memory = 2147483648.B"
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mem4gib: "memory = 4294967296.B"
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mem8gib: "memory = 8589934592.B"
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mem16gib: "memory = 17179869184.B"
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mem32gib: "memory = 34359738368.B"
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mem64gib: "memory = 68719476736.B"
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mem128gib: "memory = 137438953472.B"
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mem256gib: "memory = 274877906944.B"
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mem512gib: "memory = 549755813888.B"
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mem1tib: "memory = 1099511627776.B"
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mem2tib: "memory = 2199023255552.B"
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mem4tib: "memory = 4398046511104.B"
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mem8tib: "memory = 8796093022208.B"
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mem16tib: "memory = 17592186044416.B"
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mem32tib: "memory = 35184372088832.B"
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mem64tib: "memory = 70368744177664.B"
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mem128tib: "memory = 140737488355328.B"
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mem256tib: "memory = 281474976710656.B"
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mem512tib: "memory = 562949953421312.B"
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cpu1: "cpus = 1"
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cpu2: "cpus = 2"
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cpu5: "cpus = 5"
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cpu10: "cpus = 10"
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cpu20: "cpus = 20"
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cpu50: "cpus = 50"
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cpu100: "cpus = 100"
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cpu200: "cpus = 200"
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cpu500: "cpus = 500"
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cpu1000: "cpus = 1000"
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debug: false
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container: "docker"
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engines:
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- type: "docker"
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id: "docker"
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image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0"
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target_registry: "images.viash-hub.com"
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target_tag: "main"
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namespace_separator: "/"
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setup:
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- type: "docker"
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run:
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- "busco --version | sed 's/BUSCO\\s\\(.*\\)/busco: \"\\1\"/' > /var/software_versions.txt\n"
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entrypoint: []
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cmd: null
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- type: "native"
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id: "native"
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build_info:
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config: "src/busco/busco_run/config.vsh.yaml"
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runner: "executable"
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engine: "docker|native"
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output: "target/executable/busco/busco_run"
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executable: "target/executable/busco/busco_run/busco_run"
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viash_version: "0.9.0"
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git_commit: "7f8bcc2b3e1ffaac9778b6acb42420b19660d1a1"
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git_remote: "https://x-access-token:ghs_aSDBedV4vU66pddFDN6d8UEy0ZQApn08RAsh@github.com/viash-hub/biobox"
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git_tag: "v0.2.0-3-g7f8bcc2"
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package_config:
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name: "biobox"
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version: "main"
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description: "A collection of bioinformatics tools for working with sequence data.\n"
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info: null
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viash_version: "0.9.0"
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source: "src"
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target: "target"
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config_mods:
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- ".requirements.commands := ['ps']\n"
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- ".engines += { type: \"native\" }"
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- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
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- ".engines[.type == 'docker'].target_tag := 'main'"
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keywords:
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- "bioinformatics"
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- "modules"
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- "sequencing"
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license: "MIT"
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organization: "vsh"
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links:
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repository: "https://github.com/viash-hub/biobox"
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issue_tracker: "https://github.com/viash-hub/biobox/issues"
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