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https://github.com/MillironX/nf-core_modules.git
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f32dc15414
* update bclconvert module, as used in nf-core/demultiplex * reconfigure test with new test data * update test * formatting * update outputs, update meta * update module and test * update test config, test.yml * fix linting * emit logs and reports as dir * fix typo, recreate test.yml * fix linting Co-authored-by: CMGG ICT Team <ict@cmgg.be>
61 lines
1.7 KiB
YAML
61 lines
1.7 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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- meta:
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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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 sample FASTQ files
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pattern: "**_S*_L00?_R?_00?.fastq.gz"
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- fastq_idx:
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type: file
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description: Optional demultiplexed index FASTQ files
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pattern: "**_S*_L00?_I?_00?.fastq.gz"
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- undetermined:
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type: file
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description: Undetermined sample FASTQ files
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pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz"
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- undetermined_idx:
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type: file
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description: Optional undetermined index FASTQ files
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pattern: "Undetermined_S0_L00?_I?_00?.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: "*.{bin}"
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authors:
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- "@matthdsm"
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