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