Nextflow Registry | nf-core/arcashla/extract@0.0.0-0c7146d

nf-core/arcashla/extract @ 0.0.0-0c7146d

Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome 6 alternates.

HLA genotype RNA-seq

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @christopher-mohr

Maintainers: @christopher-mohr

Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome 6 alternates.

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

include { ARCASHLA_EXTRACT } from 'nf-core/arcashla/extract'

MIT License

Process

`Name`	`ARCASHLA_EXTRACT`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	BAM file. If the BAM file is not indexed, this tool will run samtools index before extracting reads. `*.bam`

Output 6 channels

#1 log

`*.log` file	Log file for run summary `*.log`

#2 intermediate_bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`temp_files/**.bam` file	Optional intermediate BAM file `*.bam`

#3 intermediate_sam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`temp_files/**.sam` file	Optional intermediate SAM file `*.sam`

#4 versions_arcashla tuple

`${task.process}` string	The name of the process
`arcashla` string	The name of the tool
`echo 0.5.0` eval	The expression to obtain the version of the tool

#5 extracted_reads_fastq tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.fq.gz` file	FASTQ file(s) containing chromosome 6 reads and related HLA sequences `*.fq.gz`

#6 intermediate_sorted_bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`temp_files/**.sorted.bam` file	Optional intermediate sorted BAM file `*.sorted.bam`

Tool	Description	Homepage
arcashla	arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.	https://github.com/RabadanLab/arcasHLA

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:22:32 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Farcashla%2Fextract/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/arcashla/extract/blobs/sha256:eb40584c9d8d8027d557554c5e564e39ff9cee90a2dfdd1e03f3b32a1264828b
Size	2.9 KB
Checksum	sha256:eb40584c9d8d8027d557554c5e564e39ff9cee90a2dfdd1e03f3b32a1264828b
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:22:32 (UTC)		1	2.9 KB	-