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.
Description
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.
Input
The input channel containing the FASTQ files to process and identify miRNAs.
Structure: [ val(meta), path(fastq) ]
*.fastq.gzThe input channel containing the genome FASTA files used to build the Bowtie index.
Structure: [ val(meta), path(fasta) ]
*.faThe input channel containing the Bowtie genome index directory used by the miRDeep2 mapper.
Structure: [ val(meta), path(index) ]
included in
included modules and subworkflows
maintainer
