Nextflow Registry | nf-core/portcullis/full@0.0.0-6c4ed3a

nf-core/portcullis/full @ 0.0.0-6c4ed3a

Run all Portcullis steps in one go

rnaseq genome splice junction

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @jblancoheredia

Run all Portcullis steps in one go

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

include { PORTCULLIS_FULL } from 'nf-core/portcullis/full'

MIT License

Process

`Name`	`PORTCULLIS_FULL`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing information about the sample e.g. [ id:'sample1', single_end:false ]
`bam` file	RNA-seq-aligned and sorted BAM/CRAM/SAM file `*.{bam,cram,sam}`

#2 tuple

`meta2` map	Groovy Map containing information about the sample e.g. [ id:'sample1', single_end:false ]
`bed` file	Input reference annotation of junctions in BED format `*.bed`

#3 tuple

`meta3` map	Groovy Map containing information about the sample e.g. [ id:'sample1', single_end:false ]
`fasta` file	Input genome reference fasta file `*.{fa,fasta}`

Output 8 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
`*.portcullis.log` file	Log file containing Portcullis execution details, processing steps, and filtering statistics `*.log`

#2 exon_gff tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
`*.exon.gff3` file	Output exon-based junctions in GFF format. `*.exon.gff3`

#3 versions

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

#4 intron_gff tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
`*.intron.gff3` file	Output intron-based junctions in GFF format. `*.intron.gff3`

#5 spliced_bai tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
`*.spliced.bam.bai` file	Index of the output BAM file `*spliced.bam.bai`

#6 spliced_bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
`*.spliced.bam` file	BAM file after filtering original BAM file by removing alignments associated with bad junctions `*.spliced.bam`

#7 pass_junctions_bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
`*.pass.junctions.bed` file	Filtered splice junction coordinates in BED format, containing genomic coordinates of valid splice junctions after filtering out false positives `*.pass.junctions.bed`

#8 pass_junctions_tab tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
`*.pass.junctions.tab` file	Tabular representation of filtered splice junctions with additional metrics including junction scores, read support, and filtering decision data `*.pass.junctions.tab`

Tool	Description	Homepage
portcullis	Portcullis is a tool that filters out invalid splice junctions from RNA-seq alignment data. It accepts BAM files from various RNA-seq mappers, analyzes splice junctions and removes likely false positives, outputting filtered results in multiple formats for downstream analysis.	https://portcullis.readthedocs.io/en/latest/index.html