Nextflow Registry | nf-core/paragraph/idxdepth@0.0.0-0c7146d

nf-core/paragraph/idxdepth @ 0.0.0-0c7146d

Determines the depth in a BAM/CRAM file

bam cram depth paragraph

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

Determines the depth in a BAM/CRAM file

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

include { PARAGRAPH_IDXDEPTH } from 'nf-core/paragraph/idxdepth'

MIT License

Process

`Name`	`PARAGRAPH_IDXDEPTH`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	BAM/CRAM file `*.{bam,cram}`
`input_index` file	Index of the BAM/CRAM file `*.{bai,crai}`

#2 tuple

`meta2` map	Groovy Map containing information for the fasta e.g. [ id:'test', single_end:false ]
`fasta` file	Reference genome FASTA `*.{fasta,fna,fa}`

#3 tuple

`meta3` map	Groovy Map containing information for the fasta_fai e.g. [ id:'test', single_end:false ]
`fasta_fai` file	Index of the reference genome FASTA `*.fai`

Output 3 channels

#1 depth tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.json` file	A JSON file containing depth, depth variance, read length and other parameters `*.json`

#2 versions

`versions.yml` file	File containing software versions `versions.yml`

#3 binned_depth tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.tsv` file	A TSV file containing the binned normalized depth. Can only be calculated for CRAM files `*.tsv`

Tool	Description	Homepage
paragraph	Graph realignment tools for structural variants	https://github.com/Illumina/paragraph

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:01:21 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fparagraph%2Fidxdepth/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/paragraph/idxdepth/blobs/sha256:2a035273f2b18fe999a1d21908307e409553a6e47439f83a007df8aa19c5bc3b
Size	3.0 KB
Checksum	sha256:2a035273f2b18fe999a1d21908307e409553a6e47439f83a007df8aa19c5bc3b
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:01:21 (UTC)		1	3.0 KB	-