Nextflow Registry | nf-core/ctatsplicing/startocancerintrons@0.0.0-3fc6d40

nf-core/ctatsplicing/startocancerintrons @ 0.0.0-3fc6d40

Detection and annotation of aberrant splicing isoforms in cancer transcriptomes

splicing cancer rna rnaseq

Latest version: 0.0.0-3fc6d40

Total downloads: 5

Source: nf-core/modules

Authors: @anoronh4 @nvnieuwk

Maintainers: @anoronh4

Detection and annotation of aberrant splicing isoforms in cancer transcriptomes

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

include { CTATSPLICING_STARTOCANCERINTRONS } from 'nf-core/ctatsplicing/startocancerintrons'

MIT License

Process

`Name`	`CTATSPLICING_STARTOCANCERINTRONS`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`split_junction` file	STAR alignment splice junction tab file `*.SJ.out.tab`
`junction` file	STAR alignment chimeric junction file `*.out.junction`
`bam` file	Sorted BAM/CRAM/SAM file `*.{bam,cram,sam}`
`bai` file	BAM/CRAM/SAM index file `*.{bai,crai,sai}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`genome_lib` file	CTAT genome library reference with integrated cancer intron annotation `*`

Output 12 channels

#1 chckpts tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.chckpts` file	Checkpoint files for CTAT-SPLICING, useful for debugging or resuming interrupted runs `*.chckpts`

#2 introns tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*${prefix}.introns` file	File containing all detected introns `*${prefix}.introns`

#3 igv_html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.ctat-splicing.igv.html` file	Self-contained IGV-report in HTML format for visualization of cancer introns `*.ctat-splicing.igv.html`

#4 igv_tracks tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.igv.tracks` file	IGV tracks file for visualizing cancer introns in IGV `*.igv.tracks`

#5 cancer_introns tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.cancer.introns` file	File containing detected and filtered introns that are found to be enriched in cancer transcriptomes `*.cancer.introns`

#6 introns_igv_bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.introns.for_IGV.bed` file	Bed file used as input for IGV-report visualization, containing cancer introns `*.introns.for_IGV.bed`

#7 cancer_introns_prelim tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.cancer.introns.prelim` file	File containing detected introns that have at least one supporting read and are found to be enriched in cancer transcriptomes `*.cancer.introns.prelim`

#8 gene_reads_sorted_bai tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.gene_reads.sorted.sifted.bam.bai` file	Index file for the sorted BAM of gene reads after filtering `*.gene_reads.sorted.sifted.bam.bai`

#9 gene_reads_sorted_bam tuple


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