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f4c69bc427
* bclconvert: initial commit * add most of tool * attempt at adding testing stub * add dockerfile + instructions * add container to module * update readme * more attempts at making stubs work * finish stub run * fix ci issues * more fixes to stub * add read version check to stub * fix some tests * update readme * fix version number * syntax fix * revert edit to output directory * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update meta.yaml * update thread usage * Update modules/bclconvert/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> * Escape env variable * Update modules/bclconvert/Dockerfile Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com> * fix comments by @Emiller88 * fix task.cpus Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
45 lines
1.2 KiB
YAML
45 lines
1.2 KiB
YAML
name: "bclconvert"
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description: Demultiplex Illumina BCL files
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keywords:
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- demultiplex
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- illumina
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- fastq
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tools:
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- "bclconvert":
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description: "Demultiplex Illumina BCL files"
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homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html"
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documentation: "https://support-docs.illumina.com/SW/BCL_Convert/Content/SW/FrontPages/BCL_Convert.htm"
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licence: "ILLUMINA"
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input:
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- samplesheet:
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type: file
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description: "Input samplesheet"
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pattern: "*.{csv}"
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- run_dir:
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type: directory
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description: "Input run directory containing RunInfo.xml and BCL data"
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output:
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- fastq:
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type: file
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description: Demultiplexed FASTQ files
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pattern: "*.{fastq.gz}"
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- reports:
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type: file
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description: Demultiplexing Reports
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pattern: "Reports/*.{csv,xml}"
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- logs:
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type: file
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description: Log files
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pattern: "Logs/*.{log,txt}"
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- interop:
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type: file
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description: Interop files
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pattern: "Interop/*.{bin}"
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authors:
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- "@matthdsm"
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