Nextflow Registry | nf-core/ascat@0.0.0-6c4ed3a

nf-core/ascat @ 0.0.0-6c4ed3a

copy number profiles of tumour cells.

bam copy number cram

Latest version: 0.0.0-6c4ed3a

Total downloads: 2

Source: nf-core/modules

Authors: @aasNGC @lassefolkersen @FriederikeHanssen @maxulysse @SusiJo

Maintainers: @aasNGC @lassefolkersen @FriederikeHanssen @maxulysse @SusiJo

Summary

copy number profiles of tumour cells.

Get started

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

include { ASCAT } from 'nf-core/ascat'

License

MIT License

Process

`Name`	`ASCAT`

Input 7 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input_normal` file	BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation For modifying chromosome notation in bam files please follow https://josephcckuo.wordpress.com/2016/11/17/modify-chromosome-notation-in-bam-file/. `*.{bam,cram}`
`index_normal` file	index for normal_bam/cram `*.{bai,crai}`
`input_tumor` file	BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation `*.{bam,cram}`
`index_tumor` file	index for tumor_bam/cram `*.{bai,crai}`

`allele_files` file	allele files for ASCAT WGS. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS

`loci_files` file	loci files for ASCAT WGS. Loci files without chromosome notation can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS Make sure the chromosome notation matches the bam/cram input files. To add the chromosome notation to loci files (hg19/hg38) if necessary, you can run this command `if [[ $(samtools view <your_bam_file.bam> \| head -n1 \| cut -f3)\" == \"chr\" ]]; then for i in {1..22} X; do sed -i 's/^/chr/' G1000_loci_hg19_chr_${i}.txt; done; fi`

loci_files file

loci files for ASCAT WGS. Loci files without chromosome notation can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS Make sure the chromosome notation matches the bam/cram input files. To add the chromosome notation to loci files (hg19/hg38) if necessary, you can run this command if [[ $(samtools view <your_bam_file.bam> | head -n1 | cut -f3)\" == *\"chr\"* ]]; then for i in {1..22} X; do sed -i 's/^/chr/' G1000_loci_hg19_chr_${i}.txt; done; fi

`bed_file` file	Bed file for ASCAT WES (optional, but recommended for WES)

`fasta` file	Reference fasta file (optional)

`gc_file` file	GC correction file (optional) - Used to do logR correction of the tumour sample(s) with genomic GC content

`rt_file` file	replication timing correction file (optional, provide only in combination with gc_file)

Output 10 channels

#1 png tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*png` file	ASCAT plots `*.{png}`

#2 bafs tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*BAF.txt` file	BAF file

#3 cnvs tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*cnvs.txt` file	CNV file

#4 logrs tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*LogR.txt` file	LogR file

#5 metrics tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*metrics.txt` file	File containing quality metrics `*.{metrics.txt}`

#6 segments tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*segments.txt` file	File with segments data `*.{segments.txt}`

#7 allelefreqs tuple

`meta` map