quantifies scRNA-seq data from fastq files using kb-python.
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads
:file
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
meta2
Groovy Map containing reference information e.g. [ id:‘genome’ ]
index
kb-ref index file (.idx)
*.{idx}
t2g
t2g file from kallisto
*t2g.txt
t1c
kb ref’s c1 cdna_t2c file
*.{cdna_t2c.txt}
t2c
kb ref’s c2 intron_t2c file
*.{intron_t2c.txt}
technology
:string
String value defining the sequencing technology used.
{10XV1,10XV2,10XV3,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}
workflow_mode
String value defining workflow to use, can be one of “standard”, “nac”, “lamanno” (obsolete)
{standard,lamanno,nac}
count
Groovy Map containing sample information e.g. [ id:‘test’]
*.count
kb count output folder
*.{count}
versions_kallistobustools
${task.process}
The name of the process
kallistobustools
The name of the tool
kb --version 2>&1 | sed -n 's/kb_python //p'
:eval
The expression to obtain the version of the tool
matrix
*.count/*/*.mtx
file containing the count matrix
*.mtx
versions
kallisto and bustools are wrapped in an easy-to-use program called kb
