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