Run TRUST4 on RNA-seq data
meta
:map
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
bam
:file
BAM file from bulk or single-cell RNA-seq data
*.bam
reads
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively
fasta
Path to the fasta file coordinate and sequence of V/D/J/C genes
vdj_reference
reference file of V/D/J genes
barcode_whitelist
BarocdeWhitelist file
cell_barcode_read
:string
Read containing cell barcode (either R1 or R2)
umi_read
Read containing umi barcode (either R1 or R2)
read_format
Specifies where in the read the barcodes and UMIs can be found.
tsv
*.tsv
tsv files created by TRUST4
airr_files
*_airr.tsv
TRUST4 results in AIRR format
airr_tsv
${prefix}_airr.tsv
report_tsv
*_report.tsv
TRUST4 report in tsv format
*.fa
Fasta files created by TRUST4
out
*.out
Further report files
fq
*.fq
Fastq files created by TRUST4
outs
**
output files
versions_trust4
${task.process}
The name of the process
trust4
The name of the tool
run-trust4 2>&1 | sed '/^TRUST4/!d; s/.*TRUST4 v//; s/ .*//'
:eval
The expression to obtain the version of the tool
versions
TCR and BCR assembly from bulk or single-cell RNA-seq data
