# Research Object Crate for Metagenome and metatranscriptome assembly in CWL

Original URL: https://workflowhub.eu/workflows/474/ro_crate?version=2

# 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 and co-assemblies. 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 ## Requirements - How to install This pipeline requires a conda environment with cwltool, blastn, and metaspades. If created with `requirements.yml`, the environment will be called `cwl_assembly`. ``` conda env create -f requirements.yml conda activate cwl_assembly pip install cwltool==3.1.20230601100705 ``` ## Databases You will need to pre-download fasta files for host decontamination and generate the following databases accordingly: * bwa index * blast index 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 command ```cwltool --singularity --outdir ${OUTDIR} ${CWL} ${YML}``` `$CWL` is going to be one of the executables mentioned above `$YML` should be a config yaml file including entries among what follows. You can find a yml template in the `examples` folder. ## Example output directory structure ``` Root directory ├── megahit │ └── 001 -------------------------------- Assembly root directory │ ├── assembly_stats.json ------------ Human-readable assembly stats file │ ├── coverage.tab ------------------- Coverage file │ ├── log ---------------------------- CwlToil+megahit output log | ├── options.json ------------------- Megahit input options │ ├── SRR6257420.fasta.gz ------------ Archived and trimmed assembly │ └── SRR6257420.fasta.gz.md5 -------- MD5 hash of above archive ├── metaspades │ └── 001 -------------------------------- Assembly root directory │ ├── assembly_graph.fastg ----------- Assembly graph │ ├── assembly_stats.json ------------ Human-readable assembly stats file │ ├── coverage.tab ------------------- Coverage file | ├── params.txt --------------------- Metaspades input options │ ├── spades.log --------------------- Metaspades output log │ ├── SRR6257420.fasta.gz ------------ Archived and trimmed assembly │ └── SRR6257420.fasta.gz.md5 -------- MD5 hash of above archive │ └── raw ------------------------------------ Raw data directory ├── SRR6257420.fastq.qc_stats.tsv ------ Stats for cleaned fastq ├── SRR6257420_fastp_clean_1.fastq.gz -- Cleaned paired-end file_1 └── SRR6257420_fastp_clean_2.fastq.gz -- Cleaned paired-end file_2 ```

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## Contents

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