mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
69 lines
2 KiB
YAML
69 lines
2 KiB
YAML
|
name: "bases2fastq"
|
||
|
|
description: Demultiplex Element Biosciences bases files
|
||
|
|
keywords:
|
||
|
|
- demultiplex
|
||
|
|
- element
|
||
|
|
- fastq
|
||
|
|
tools:
|
||
|
|
- "bases2fastq":
|
||
|
|
description: "Demultiplexes sequencing data and converts base calls into FASTQ files for secondary analysis"
|
||
|
|
homepage: "https://go.elementbiosciences.com/bases2fastq-download"
|
||
|
|
documentation: "https://www.elementbiosciences.com/resources/user-guides/workflow/bases2fastq"
|
||
|
|
licence: "http://go.elembio.link/eula"
|
||
|
|
|
||
|
|
input:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- run_manifest:
|
||
|
|
type: file
|
||
|
|
description: RunManifest file
|
||
|
|
pattern: "*.{csv}"
|
||
|
|
- run_dir:
|
||
|
|
type: directory
|
||
|
|
description: "Input run directory containing optionally containing a RunManifest.json if run_manifest is not supplied"
|
||
|
|
|
||
|
|
output:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- versions:
|
||
|
|
type: file
|
||
|
|
description: File containing software versions
|
||
|
|
pattern: "versions.yml"
|
||
|
|
- sample_fastq:
|
||
|
|
type: file
|
||
|
|
description: Demultiplexed sample FASTQ files
|
||
|
|
pattern: "output/Samples/*/*_R*.fastq.gz"
|
||
|
|
- sample_json:
|
||
|
|
type: file
|
||
|
|
description: Demultiplexed sample stats
|
||
|
|
pattern: "output/Samples/*/*.json"
|
||
|
|
- qc_report:
|
||
|
|
type: file
|
||
|
|
description: QC HTML report
|
||
|
|
pattern: "output/*.html"
|
||
|
|
- run_stats:
|
||
|
|
type: file
|
||
|
|
description: QC HTML report
|
||
|
|
pattern: "output/*.html"
|
||
|
|
- generated_run_manifest:
|
||
|
|
type: file
|
||
|
|
description: Updated Run Manifest JSON from the run_manifest csv
|
||
|
|
pattern: "output/RunManifest.json"
|
||
|
|
- metrics:
|
||
|
|
type: file
|
||
|
|
description: Sample metrics
|
||
|
|
pattern: "output/Metrics.csv"
|
||
|
|
- unassigned:
|
||
|
|
type: file
|
||
|
|
description: Unassigned Sequences
|
||
|
|
pattern: "output/UnassignedSequences.csv"
|
||
|
|
|
||
|
|
authors:
|
||
|
|
- "@Emiller88"
|