Demultiplex Element Biosciences bases files
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
run_manifest
:file
RunManifest file
*.{csv}
run_dir
:directory
Input run directory containing optionally containing a RunManifest.json if run_manifest is not supplied
sample_fastq
output/Samples/**/*_R*.fastq.gz
Demultiplexed sample FASTQ files
output/Samples/*/*_R*.fastq.gz
sample_json
output/Samples/**/*_stats.json
Demultiplexed sample stats
output/Samples/*/*.json
qc_report
output/*_QC.html
QC HTML report
output//*_QC.html
multiqc_report
output/multiqc_report.html
Multiqc HTML report
run_stats
output/RunStats.json
output/*.html
generated_run_manifest
output/RunManifest.json
Updated Run Manifest JSON from the run_manifest csv
metrics
output/Metrics.csv
Sample metrics
unassigned
output/UnassignedSequences.csv
Unassigned Sequences
versions
versions.yml
File containing software versions
Demultiplexes sequencing data and converts base calls into FASTQ files for secondary analysis
