Description

Run TRUST4 on RNA-seq data

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

bam:file

BAM file from bulk or single-cell RNA-seq data

*.bam

reads:file

List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively

fasta:file

Path to the fasta file coordinate and sequence of V/D/J/C genes

vdj_reference:file

reference file of V/D/J genes

cell_barcode_read:string

Read containing cell barcode (either R1 or R2)

umi_read:string

Read containing umi barcode (either R1 or R2)

barcode_whitelist:file

BarocdeWhitelist file

Output

name:type
description
pattern

tsv

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.tsv:file

tsv files created by TRUST4

*.tsv

airr_files

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*_airr.tsv:file

TRUST4 results in AIRR format

*_airr.tsv

airr_tsv

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${meta.id}_airr.tsv:file

TRUST4 results in AIRR format

*_airr.tsv

report_tsv

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*_report.tsv:file

TRUST4 report in tsv format

*_report.tsv

fasta

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.fa:file

Fasta files created by TRUST4

*.fa

out

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.out:file

Further report files

*.out

fq

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.fq:file

Fastq files created by TRUST4

*.fq

outs

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

**:file

outputt files

versions

versions.yml:file

File containing software versions

versions.yml

Tools

trust4
GPL v3

TCR and BCR assembly from bulk or single-cell RNA-seq data