Run TRUST4 on RNA-seq data
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
bam{:bash}
:file
BAM file from bulk or single-cell RNA-seq data
*.bam
reads{:bash}
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively
fasta{:bash}
Path to the fasta file coordinate and sequence of V/D/J/C genes
vdj_reference{:bash}
reference file of V/D/J genes
barcode_whitelist{:bash}
BarocdeWhitelist file
cell_barcode_read{:bash}
:string
Read containing cell barcode (either R1 or R2)
umi_read{:bash}
Read containing umi barcode (either R1 or R2)
read_format{:bash}
Specifies where in the read the barcodes and UMIs can be found.
tsv{:bash}
*.tsv{:bash}
tsv files created by TRUST4
*.tsv
airr_files{:bash}
*_airr.tsv{:bash}
TRUST4 results in AIRR format
*_airr.tsv
airr_tsv{:bash}
${meta.id}_airr.tsv{:bash}
report_tsv{:bash}
*_report.tsv{:bash}
TRUST4 report in tsv format
*_report.tsv
*.fa{:bash}
Fasta files created by TRUST4
*.fa
out{:bash}
*.out{:bash}
Further report files
*.out
fq{:bash}
*.fq{:bash}
Fastq files created by TRUST4
*.fq
outs{:bash}
**{:bash}
outputt files
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
TCR and BCR assembly from bulk or single-cell RNA-seq data
