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>
446 lines
12 KiB
YAML
446 lines
12 KiB
YAML
name: "bcl_convert"
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version: "main"
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authors:
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- name: "Toni Verbeiren"
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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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github: "tverbeiren"
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linkedin: "verbeiren"
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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 and CEO"
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- name: "Dorien Roosen"
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roles:
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- "author"
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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: "Input arguments"
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arguments:
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- type: "file"
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name: "--bcl_input_directory"
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alternatives:
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- "-i"
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description: "Input run directory"
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info: null
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example:
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- "bcl_dir"
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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: "file"
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name: "--sample_sheet"
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alternatives:
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- "-s"
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description: "Path to SampleSheet.csv file (default searched for in --bcl_input_directory)"
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info: null
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example:
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- "bcl_dir/sample_sheet.csv"
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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: "input"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--run_info"
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description: "Path to RunInfo.xml file (default root of BCL input directory)"
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info: null
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example:
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- "bcl_dir/RunInfo.xml"
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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: "input"
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multiple: false
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multiple_sep: ";"
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- name: "Lane and tile settings"
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arguments:
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- type: "integer"
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name: "--bcl_only_lane"
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description: "Convert only specified lane number (default all lanes)"
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info: null
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example:
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- 1
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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"
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name: "--first_tile_only"
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description: "Only convert first tile of input (for testing & debugging)"
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info: null
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example:
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- true
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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: "--tiles"
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description: "Process only a subset of tiles by a regular expression"
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info: null
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example:
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- "s_[0-9]+_1"
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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: "--exclude_tiles"
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description: "Exclude set of tiles by a regular expression"
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info: null
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example:
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- "s_[0-9]+_1"
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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: "Resource arguments"
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arguments:
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- type: "boolean"
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name: "--shared_thread_odirect_output"
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description: "Use linux native asynchronous io (io_submit) for file output (Default=false)"
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info: null
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example:
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- true
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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: "--bcl_num_parallel_tiles"
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description: "\\# of tiles to process in parallel (default 1)"
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info: null
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example:
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- 1
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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: "--bcl_num_conversion_threads"
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description: "\\# of threads for conversion (per tile, default # cpu threads)"
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info: null
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example:
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- 1
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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: "--bcl_num_compression_threads"
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description: "\\# of threads for fastq.gz output compression (per tile, default\
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\ # cpu threads, or HW+12)"
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info: null
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example:
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- 1
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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: "--bcl_num_decompression_threads"
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description: "\\# of threads for bcl/cbcl input decompression (per tile, default\
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\ half # cpu threads, or HW+8). Only applies when preloading files"
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info: null
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example:
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- 1
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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: "Run arguments"
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arguments:
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- type: "boolean"
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name: "--bcl_only_matched_reads"
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description: "For pure BCL conversion, do not output files for 'Undetermined'\
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\ [unmatched] reads (output by default)"
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info: null
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example:
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- true
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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"
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name: "--no_lane_splitting"
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description: "Do not split FASTQ file by lane (false by default)"
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info: null
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example:
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- true
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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: "--num_unknown_barcodes_reported"
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description: "\\# of Top Unknown Barcodes to output (1000 by default)"
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info: null
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example:
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- 1000
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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"
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name: "--bcl_validate_sample_sheet_only"
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description: "Only validate RunInfo.xml & SampleSheet files (produce no FASTQ\
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\ files)"
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info: null
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example:
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- true
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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"
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name: "--strict_mode"
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description: "Abort if any files are missing (false by default)"
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info: null
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example:
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- true
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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"
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name: "--sample_name_column_enabled"
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description: "Use sample sheet 'Sample_Name' column when naming fastq files &\
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\ subdirectories"
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info: null
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example:
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- true
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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: "Output arguments"
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arguments:
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- type: "file"
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name: "--output_directory"
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alternatives:
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- "-o"
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description: "Output directory containig fastq files"
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info: null
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example:
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- "fastq_dir"
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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: "output"
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multiple: false
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multiple_sep: ";"
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- type: "boolean"
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name: "--bcl_sampleproject_subdirectories"
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description: "Output to subdirectories based upon sample sheet 'Sample_Project'\
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\ column"
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info: null
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example:
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- true
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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: "--fastq_gzip_compression_level"
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description: "Set fastq output compression level 0-9 (default 1)"
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info: null
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example:
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- 1
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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: "file"
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name: "--reports"
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description: "Reports directory"
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info: null
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example:
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- "reports_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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- type: "file"
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name: "--logs"
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description: "Reports directory"
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info: null
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example:
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- "logs_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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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: "Convert bcl files to fastq files using bcl-convert.\nInformation about\
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\ upgrading from bcl2fastq via\n[Upgrading from bcl2fastq to BCL Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)\n\
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and [BCL Convert Compatible Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)\n"
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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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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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- "demultiplex"
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- "fastq"
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- "bcl"
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- "illumina"
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license: "Proprietary"
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links:
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repository: "https://github.com/viash-hub/biobox"
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homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html"
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documentation: "https://support.illumina.com/downloads/bcl-convert-user-guide.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: "debian:trixie-slim"
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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: "apt"
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packages:
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- "wget"
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- "gdb"
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- "which"
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- "hostname"
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- "alien"
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- "procps"
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interactive: false
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- type: "docker"
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run:
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- "wget https://s3.amazonaws.com/webdata.illumina.com/downloads/software/bcl-convert/bcl-convert-4.2.7-2.el8.x86_64.rpm\
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\ -O /tmp/bcl-convert.rpm && \\\nalien -i /tmp/bcl-convert.rpm && \\\nrm -rf\
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\ /var/lib/apt/lists/* && \\\nrm /tmp/bcl-convert.rpm\n"
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- type: "docker"
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run:
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- "echo \"bcl-convert: \\\"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/\
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\ s/^bcl-convert\\ Version //p')\\\"\" > /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/bcl_convert/config.vsh.yaml"
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runner: "executable"
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engine: "docker|native"
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output: "target/executable/bcl_convert"
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executable: "target/executable/bcl_convert/bcl_convert"
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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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