bam_stats_mirna_mirtop

mirtop is a command line tool to annotate miRNAs and isomiRs and compute general statistics using the mirGFF3 format.

miRNAisomirsbamstats

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

Description

mirtop is a command line tool to annotate miRNAs and isomiRs and compute general statistics using the mirGFF3 format.

Input

name

description

pattern

`ch_bam`

The input channel containing the BAM/CRAM/SAM files
Structure: [ val(meta), path(bam) ]

*.{bam/cram/sam}

`ch_hairpin`

Input channel containing the hairpin fasta file
Structure: [ val(meta), path(fasta) ]

*.{fasta,fa}

`ch_gtf_species`

Input channel containing the species gtf and the name of species in miRbase format
Structure: [ val(meta), path(gtf), val(species)]

*.{gtf}

Output

name

description

pattern

`isomirs`

Channel containing isomiRs compatible files
Structure: [ val(meta), path(tsv) ]

*.tsv

`counts`

Channel containing TSV files with the miRNA and isomiR counts per sample
Structure: [ val(meta), path(tsv) ]

*.tsv

`stats_txt`

Channel containing TXT file with a table with different statistics for each type of isomiRs: total counts, average counts, total sequences.
Structure: [ val(meta), path(txt) ]

*.txt

`stats_log`

Channel containing log files in JSON format with the same information as stats_txt
Structure: [ val(meta), path(log) ]

*.log