Nextflow Registry | nf-core/slamdunk/all@0.0.0-6c4ed3a

nf-core/slamdunk/all @ 0.0.0-6c4ed3a

Complete SLAMseq analysis pipeline including read mapping, filtering, SNP calling, and quantification

slamseq rna-seq mapping snp quantification

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @haidyi

Maintainers: @haidyi

Complete SLAMseq analysis pipeline including read mapping, filtering, SNP calling, and quantification

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

include { SLAMDUNK_ALL } from 'nf-core/slamdunk/all'

MIT License

Process

`Name`	`SLAMDUNK_ALL`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`input` file	Input FASTQ file(s) for SLAMseq analysis `*.{bam,fastq,fq,fastq.gz,fq.gz}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. `[ id:'reference' ]`
`fasta` file	Reference genome FASTA file `*.{fasta,fa,fas,fna}`

#3 tuple

`meta3` map	Groovy Map containing annotation information e.g. `[ id:'annotation' ]`
`bed` file	BED file with 3'UTR coordinates `*.bed`

#4 tuple

`meta4` map	Groovy Map containing annotation information e.g. `[ id:'annotation' ]`
`filter_bed` file	BED file with 3'UTR coordinates to filter multimappers `*.bed`

Output 8 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`outputs/map/*.bam` file	Mapped BAM file `*.bam`

#2 tsv tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`outputs/count/*.tsv` file	TSV file with T>C conversion counts and rates `*.tsv`

#3 vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`outputs/snp/*.vcf` file	VCF file containing called SNPs/variants `*.vcf`

#4 versions

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

#5 filtered_bai tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`outputs/filter/*.bam.bai` file	BAM index file for filtered BAM `*.bam.bai`

#6 filtered_bam tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`outputs/filter/*.bam` file	Filtered BAM file with multimapper and PCR duplicate removal `*.bam`

#7 mins_bedgraph tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`outputs/count/*_mins.bedgraph` file	BedGraph file with coverage on minus strand `*_mins.bedgraph`

#8 plus_bedgraph tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`outputs/count/*_plus.bedgraph` file	BedGraph file with coverage on plus strand `*_plus.bedgraph`

Tool	Description	Homepage
slamdunk	Slamdunk is a software tool for SLAMseq data analysis that performs mapping, filtering, SNP calling, and quantification of metabolic RNA labeling experiments.	http://t-neumann.github.io/slamdunk/docs.html