Description

Demultiplex Element Biosciences bases files

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

run_manifest (file)

RunManifest file

*.{csv}

run_dir (directory)

Input run directory containing optionally containing a RunManifest.json if run_manifest is not supplied

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

sample_fastq (file)

Demultiplexed sample FASTQ files

output/Samples/*/*_R*.fastq.gz

sample_json (file)

Demultiplexed sample stats

output/Samples/*/*.json

qc_report (file)

QC HTML report

output/*.html

run_stats (file)

QC HTML report

output/*.html

generated_run_manifest (file)

Updated Run Manifest JSON from the run_manifest csv

output/RunManifest.json

metrics (file)

Sample metrics

output/Metrics.csv

unassigned (file)

Unassigned Sequences

output/UnassignedSequences.csv
included in
demultiplex
author
Github user Emiller88
get in touch
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Tools

bases2fastq
http://go.elembio.link/eula

Demultiplexes sequencing data and converts base calls into FASTQ files for secondary analysis

go.elementbiosciences.com/bases2fastq-download elementbiosciences.com/resources/user-guides/workflow/bases2fastq