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
Version History
master @ 39efebc (latest) Created 21st Jun 2023 at 11:41 by Germana Baldi
Merge pull request #8 from EBI-Metagenomics/readme_requirements
Update of README, examples, and installation requirements
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master
39efebc
master @ b269a55 (earliest) Created 19th May 2023 at 14:59 by Varsha Kale
Update README.md
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Views: 2531 Downloads: 292
Created: 19th May 2023 at 14:59
Last updated: 21st Jun 2023 at 11:41
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