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nf-core/t1k/run @ 0.0.0-6c4ed3a

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polymorphic genes HLA Kir
Latest version: 0.0.0-6c4ed3a
Total downloads: 7
Source: nf-core/modules
Authors: @georgiakes
Maintainers: @georgiakes

Summary

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Get started

Add the following snippet to your workflow script to include this module.

include { T1K_RUN } from 'nf-core/t1k/run'

License

MIT License

Process
Name T1K_RUN
Input 1 channel
#1 tuple
meta map

Groovy Map containing sample id and single_end label for fastq input files. e.g. [ id:'sample1', single_end:false ]
input file

BAM or FASTQ file(s).

 *.{bam,fastq}
fasta file

Reference fasta file.

 *.{fa,fasta}
cordinates file

A fasta file with the coordinates of the gene alleles in the header as created form the t1k/build

 *.fa
barcodes file

A file with a list of barcodes.

 *.txt
barcodewhitelist file

A file with a whitelist of barcodes.

 *.txt
Output 10 channels
#1 allele_tsv tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*_allele.tsv file

File with the representative alleles and their quality scores.

 *_allele.tsv
#2 allele_vcf tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*_allele.vcf file

A vcf file with the novel SNPs.
#3 barcode_tsv tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*_barcode_expr.tsv file

Data matrix where rows are the barcodes and columns are the allele abundances.
#4 genotype_tsv tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*_genotype.tsv file

Genotyping file where the allele for each gene has its own line.

 *_genotype.tsv
#5 versions_t1k tuple
${task.process} string

The name of the process
t1k string

The name of the tool
run-t1k 2>&1 | head -n 1 | cut -d '-' -f 1 | cut -d v -f 2 eval

The expression to obtain the version of the tool
#6 barcode_aligned tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*_aligned_bc.fa file

Barcodes form aligned reads.

 *_aligned_bc.fa
#7 candidate_reads tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*_candidate*.fq file

Fastq file containing candidate reads extracted from raw data for genotyping.
#8 barcode_candidate tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*_candidate_bc.fa file

Barcodes form candidate reads.

 *_candidate_bc.fa
#9 aligned_reads_paired tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*_aligned_{1,2}.fa file

Aligned reads in fasta format from paired-end input.

 *_aligned_{1,2}.fa
#10 aligned_reads_single tuple
meta map