cellgeni/preprocess_tiles

subworkflow

Sort SAM/BAM/CRAM file

sort bam sam cram

Module Information

Repository: https://github.com/cellgeni/nf-modules/tree/main/subworkflows/sanger-cellgeni/preprocess_tiles
Source: Sanger (cellgeni)
Organization: cellgeni
Authors: @BioinfoTongLI
Maintainers: @BioinfoTongLI

This subworkflow uses the following modules:

samtools/sort samtools/index

Name	Type	Description
ch_bam	file	The input channel containing the BAM/CRAM/SAM files Structure: [ val(meta), path(bam) ]

Name	Type	Description
bam	file	Channel containing BAM files Structure: [ val(meta), path(bam) ]
bai	file	Channel containing indexed BAM (BAI) files Structure: [ val(meta), path(bai) ]
csi	file	Channel containing CSI files Structure: [ val(meta), path(csi) ]
versions	file	File containing software versions Structure: [ path(versions.yml) ]

Include this subworkflow in your Nextflow pipeline:

include { PREPROCESS_TILES } from 'https://github.com/cellgeni/nf-modules/tree/main/subworkflows/sanger-cellgeni/preprocess_tiles'