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: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
barcode_whitelist:file
BarocdeWhitelist file
cell_barcode_read:string
Read containing cell barcode (either R1 or R2)
umi_read:string
Read containing umi barcode (either R1 or R2)
read_format:string
Specifies where in the read the barcodes and UMIs can be found.
tsv
*.tsv:file
tsv files created by TRUST4
*.tsv
airr_files
*_airr.tsv:file
TRUST4 results in AIRR format
*_airr.tsv
airr_tsv
${meta.id}_airr.tsv:file
report_tsv
*_report.tsv:file
TRUST4 report in tsv format
*_report.tsv
fasta
*.fa:file
Fasta files created by TRUST4
*.fa
out
*.out:file
Further report files
*.out
fq
*.fq:file
Fastq files created by TRUST4
*.fq
outs
**:file
outputt files
versions
versions.yml:file
File containing software versions
versions.yml
TCR and BCR assembly from bulk or single-cell RNA-seq data
