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62 lines
1.8 KiB
YAML
62 lines
1.8 KiB
YAML
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name: "bcl2fastq"
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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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- "bcl2fastq":
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description: "Demultiplex Illumina BCL files"
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homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software"
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documentation: "https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2-v2-20-software-guide-15051736-03.pdf"
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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: Optional 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/*"
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- stats:
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type: file
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description: Statistics files
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pattern: "Stats/*"
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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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