# Research Object Crate for Metagenome and metatranscriptome assembly in CWL

Original URL: https://workflowhub.eu/workflows/474/ro_crate?version=1

# CWL-assembly [![Codacy Badge](https://api.codacy.com/project/badge/Grade/684724bbc0134960ab41748f4a4b732f)](https://www.codacy.com/app/mb1069/CWL-assembly?utm_source=github.com&utm_medium=referral&utm_content=EBI-Metagenomics/CWL-assembly&utm_campaign=Badge_Grade) [![Build Status](https://travis-ci.org/EBI-Metagenomics/CWL-assembly.svg?branch=develop)](https://travis-ci.org/EBI-Metagenomics/CWL-assembly) ## Description This repository contains two workflows for metagenome and metatranscriptome assembly of short read data. MetaSPAdes is used as default for paired end data, and MEGAHIT for single end data. MEGAHIT can be specified as the default assembler in the yaml file if preferred. Steps include: QC - removal of short reads, low quality regions, adapters and host decontamination Assembly - with metaSPADES or MEGAHIT Post-assembly - Host and PhiX decontamination, contig length filter (500bp), stats generation. Multiple input read files can also be specified for co-assembly. ## Requirements This pipeline requires and environment with cwltool, blastn, metaspades and megahit. ## Databases Predownload fasta files for host decontamination and generate: - bwa index folder - blast index folder Specify the locations in the yaml file when running the pipeline. ## Main pipeline executables src/workflows/metagenome_pipeline.cwl src/workflows/metatranscriptome_pipeline.cwl # Example output directory structure ``` SRP0741 └── SRP074153 Project directory containing all assemblies under that project ├── downloads.yml Raw data download caching logfile, to avoid duplicate downloads of raw data ├── SRR6257 │ └── SRR6257420 Run directory │ └── megahit │ ├── 001 Assembly directory │ │ ├── SRR6257420.fasta Trimmed assembly │ │ ├── SRR6257420.fasta.gz Archive trimmed assembly │ │ ├── SRR6257420.fasta.gz.md5 MD5 hash of above archive │ │ ├── coverage.tab Coverage file │ │ ├── final.contigs.fa Raw assembly │ │ ├── job_config.yml CWL job configuration │ │ ├── megahit.log Assembler output log │ │ ├── output.json Human-readable Assembly stats file │ │ ├── sorted.bam BAM file of assembly │ │ ├── sorted.bam.bai Secondary BAM file │ │ └── toil.log cwlToil output log │ └── metaspades Assembly of equivalent data using another assembler (eg metaspades, spades...) │ └── ... │ ├── raw Raw data directory │ └── SRR6257420.fastq.gz Raw data files │ └── tmp Temporary directory for assemblies └── SRR6257 └── SRR6257420 └── megahit └── 001 ```

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License
  CC-BY-4.0

## Contents

Main Workflow: Metagenome and metatranscriptome assembly in CWL
Size: 6441 bytes