sortmerna

Description

Local sequence alignment tool for filtering, mapping and clustering. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files.

Type

bash_script

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
sortmerna_log: "$id.$key.sortmerna_log"  
fastq_1: "$id.$key.fastq_1"  
fastq_2: "$id.$key.fastq_2"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/rnaseq.git \  
  -revision v0.3.0 \  
  -main-script target/nextflow/sortmerna/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--paired	boolean	Are the reads single-end or paired-end
--input	file multiple	Input fastq
--ribo_database_manifest	file multiple	Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA.

Name

Type & Properties

--paired

boolean

--input

file

multiple

--ribo_database_manifest

file

multiple

Output

Name	Type & Properties	Description
--sortmerna_log	file output	Sortmerna log file.
--fastq_1	file required output	Output file for read 1.
--fastq_2	file output	Output file for read 2.

Name

Type & Properties

--sortmerna_log

file

output

--fastq_1

file

required

output

--fastq_2

file

output