fastq_find_mirna_mirdeep2

This subworkflow identifies miRNAs from FASTQ files using miRDeep2. The workflow converts FASTQ to FASTA, processes and replaces any whitespace in sequence IDs, builds a Bowtie index of the genome, and then maps reads using miRDeep2 mapper before identifying known and novel miRNAs.

miRNAFASTQFASTABowtiemiRDeep2

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/fastq_find_mirna_mirdeep2

Description

Input

name

description

pattern

`ch_reads`

The input channel containing the FASTQ files to process and identify miRNAs.
Structure: [ val(meta), path(fastq) ]

*.fastq.gz

`ch_genome_fasta`

The input channel containing the genome FASTA files used to build the Bowtie index.
Structure: [ val(meta), path(fasta) ]

*.fa

`ch_mirna_mature_hairpin`

The input channel containing the mature and hairpin miRNA sequences for miRNA identification.
Structure: [ val(meta), path(mature_fasta), path(hairpin_fasta) ]

*.fa

Output

name

description

pattern

`outputs`

The output channel containing the BED, CSV, and HTML files with the identified miRNAs.
Structure: [ val(meta), path(bed), path(csv), path(html) ]

*.{bed,csv,html}

`versions`

File containing software versions
Structure: [ path(versions.yml) ]

versions.yml

fastq_find_mirna_mirdeep2

Description

Input

`ch_reads`

`ch_genome_fasta`

`ch_mirna_mature_hairpin`

Output

`outputs`

`versions`

included in

included modules and subworkflows

maintainer

get in touch