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      "description": "# CWL-assembly\n[![Codacy Badge](https://api.codacy.com/project/badge/Grade/684724bbc0134960ab41748f4a4b732f)](https://www.codacy.com/app/mb1069/CWL-assembly?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=EBI-Metagenomics/CWL-assembly&amp;utm_campaign=Badge_Grade)\n[![Build Status](https://travis-ci.org/EBI-Metagenomics/CWL-assembly.svg?branch=develop)](https://travis-ci.org/EBI-Metagenomics/CWL-assembly)\n\n## Description\n\nThis 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:\n\n  * _QC_: removal of short reads, low quality regions, adapters and host decontamination\n  * _Assembly_: with metaSPADES or MEGAHIT\n  * _Post-assembly_: Host and PhiX decontamination, contig length filter (500bp), stats generation\n\n## Requirements - How to install\n\nThis pipeline requires a conda environment with cwltool, blastn, and metaspades. If created with `requirements.yml`, the environment will be called `cwl_assembly`. \n\n```\nconda env create -f requirements.yml\nconda activate cwl_assembly\npip install cwltool==3.1.20230601100705\n```\n\n## Databases\n\nYou will need to pre-download fasta files for host decontamination and generate the following databases accordingly:\n  * bwa index\n  * blast index\n    \nSpecify the locations in the yaml file when running the pipeline.\n\n## Main pipeline executables\n\n  * `src/workflows/metagenome_pipeline.cwl`\n  * `src/workflows/metatranscriptome_pipeline.cwl`\n\n## Example command\n\n```cwltool --singularity --outdir ${OUTDIR} ${CWL} ${YML}```\n\n`$CWL` is going to be one of the executables mentioned above\n`$YML` should be a config yaml file including entries among what follows. \nYou can find a yml template in the `examples` folder.\n\n## Example output directory structure\n```\nRoot directory\n    ├── megahit\n    │   └── 001 -------------------------------- Assembly root directory\n    │       ├── assembly_stats.json ------------ Human-readable assembly stats file\n    │       ├── coverage.tab ------------------- Coverage file\n    │       ├── log ---------------------------- CwlToil+megahit output log\n    |       ├── options.json ------------------- Megahit input options\n    │       ├── SRR6257420.fasta.gz ------------ Archived and trimmed assembly\n    │       └── SRR6257420.fasta.gz.md5 -------- MD5 hash of above archive\n    ├── metaspades\n    │   └── 001 -------------------------------- Assembly root directory\n    │       ├── assembly_graph.fastg ----------- Assembly graph\n    │       ├── assembly_stats.json ------------ Human-readable assembly stats file\n    │       ├── coverage.tab ------------------- Coverage file\n    |       ├── params.txt --------------------- Metaspades input options\n    │       ├── spades.log --------------------- Metaspades output log\n    │       ├── SRR6257420.fasta.gz ------------ Archived and trimmed assembly\n    │       └── SRR6257420.fasta.gz.md5 -------- MD5 hash of above archive\n    │&nbsp;\n    └── raw ------------------------------------ Raw data directory\n        ├── SRR6257420.fastq.qc_stats.tsv ------ Stats for cleaned fastq\n        ├── SRR6257420_fastp_clean_1.fastq.gz -- Cleaned paired-end file_1\n        └── SRR6257420_fastp_clean_2.fastq.gz -- Cleaned paired-end file_2\n```\n",
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      "description": "# CWL-assembly\n[![Codacy Badge](https://api.codacy.com/project/badge/Grade/684724bbc0134960ab41748f4a4b732f)](https://www.codacy.com/app/mb1069/CWL-assembly?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=EBI-Metagenomics/CWL-assembly&amp;utm_campaign=Badge_Grade)\n[![Build Status](https://travis-ci.org/EBI-Metagenomics/CWL-assembly.svg?branch=develop)](https://travis-ci.org/EBI-Metagenomics/CWL-assembly)\n\n## Description\n\nThis 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:\n\n  * _QC_: removal of short reads, low quality regions, adapters and host decontamination\n  * _Assembly_: with metaSPADES or MEGAHIT\n  * _Post-assembly_: Host and PhiX decontamination, contig length filter (500bp), stats generation\n\n## Requirements - How to install\n\nThis pipeline requires a conda environment with cwltool, blastn, and metaspades. If created with `requirements.yml`, the environment will be called `cwl_assembly`. \n\n```\nconda env create -f requirements.yml\nconda activate cwl_assembly\npip install cwltool==3.1.20230601100705\n```\n\n## Databases\n\nYou will need to pre-download fasta files for host decontamination and generate the following databases accordingly:\n  * bwa index\n  * blast index\n    \nSpecify the locations in the yaml file when running the pipeline.\n\n## Main pipeline executables\n\n  * `src/workflows/metagenome_pipeline.cwl`\n  * `src/workflows/metatranscriptome_pipeline.cwl`\n\n## Example command\n\n```cwltool --singularity --outdir ${OUTDIR} ${CWL} ${YML}```\n\n`$CWL` is going to be one of the executables mentioned above\n`$YML` should be a config yaml file including entries among what follows. \nYou can find a yml template in the `examples` folder.\n\n## Example output directory structure\n```\nRoot directory\n    ├── megahit\n    │   └── 001 -------------------------------- Assembly root directory\n    │       ├── assembly_stats.json ------------ Human-readable assembly stats file\n    │       ├── coverage.tab ------------------- Coverage file\n    │       ├── log ---------------------------- CwlToil+megahit output log\n    |       ├── options.json ------------------- Megahit input options\n    │       ├── SRR6257420.fasta.gz ------------ Archived and trimmed assembly\n    │       └── SRR6257420.fasta.gz.md5 -------- MD5 hash of above archive\n    ├── metaspades\n    │   └── 001 -------------------------------- Assembly root directory\n    │       ├── assembly_graph.fastg ----------- Assembly graph\n    │       ├── assembly_stats.json ------------ Human-readable assembly stats file\n    │       ├── coverage.tab ------------------- Coverage file\n    |       ├── params.txt --------------------- Metaspades input options\n    │       ├── spades.log --------------------- Metaspades output log\n    │       ├── SRR6257420.fasta.gz ------------ Archived and trimmed assembly\n    │       └── SRR6257420.fasta.gz.md5 -------- MD5 hash of above archive\n    │&nbsp;\n    └── raw ------------------------------------ Raw data directory\n        ├── SRR6257420.fastq.qc_stats.tsv ------ Stats for cleaned fastq\n        ├── SRR6257420_fastp_clean_1.fastq.gz -- Cleaned paired-end file_1\n        └── SRR6257420_fastp_clean_2.fastq.gz -- Cleaned paired-end file_2\n```\n",
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