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69 lines
2 KiB
YAML
69 lines
2 KiB
YAML
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name: "bases2fastq"
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description: Demultiplex Element Biosciences bases files
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keywords:
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- demultiplex
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- element
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- fastq
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tools:
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- "bases2fastq":
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description: "Demultiplexes sequencing data and converts base calls into FASTQ files for secondary analysis"
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homepage: "https://go.elementbiosciences.com/bases2fastq-download"
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documentation: "https://www.elementbiosciences.com/resources/user-guides/workflow/bases2fastq"
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licence: "http://go.elembio.link/eula"
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input:
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- meta:
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type: map
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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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- run_manifest:
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type: file
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description: RunManifest file
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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 optionally containing a RunManifest.json if run_manifest is not supplied"
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output:
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- meta:
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type: map
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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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- 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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- sample_fastq:
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type: file
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description: Demultiplexed sample FASTQ files
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pattern: "output/Samples/*/*_R*.fastq.gz"
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- sample_json:
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type: file
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description: Demultiplexed sample stats
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pattern: "output/Samples/*/*.json"
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- qc_report:
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type: file
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description: QC HTML report
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pattern: "output/*.html"
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- run_stats:
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type: file
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description: QC HTML report
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pattern: "output/*.html"
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- generated_run_manifest:
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type: file
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description: Updated Run Manifest JSON from the run_manifest csv
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pattern: "output/RunManifest.json"
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- metrics:
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type: file
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description: Sample metrics
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pattern: "output/Metrics.csv"
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- unassigned:
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type: file
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description: Unassigned Sequences
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pattern: "output/UnassignedSequences.csv"
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authors:
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- "@Emiller88"
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