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
${prefix}/Samples/**/*_R*.fastq.gz
Demultiplexed sample FASTQ files
${prefix}/Samples/*/*_R*.fastq.gz
sample_json
${prefix}/Samples/**/*_stats.json
Demultiplexed sample stats
${prefix}/Samples/*/*.json
qc_report
${prefix}/*_QC.html
QC HTML report
${prefix}//*_QC.html
multiqc_report
${prefix}/multiqc_report.html
Multiqc HTML report
run_stats
${prefix}/RunStats.json
${prefix}/*.html
generated_run_manifest
${prefix}/RunManifest.json
Updated Run Manifest JSON from the run_manifest csv
metrics
${prefix}/Metrics.csv
Sample metrics
unassigned
${prefix}/UnassignedSequences.csv
Unassigned Sequences
versions_bases2fastq
${task.process}
:string
The process the versions were collected from
bases2fastq
The tool name
bases2fastq --version | sed "s/.*version //;s/,.*//"
The command used to generate the version of the tool
versions
Demultiplexes sequencing data and converts base calls into FASTQ files for secondary analysis
