{"repo":"nf-core/fetchngs","free":true,"listed":false,"github":"https://github.com/nf-core/fetchngs","clone":"git clone https://github.com/nf-core/fetchngs.git","description":"Pipeline to fetch metadata and raw FastQ files from public databases","language":"Nextflow","stars":200,"topics":["workflow","nextflow","nf-core","pipeline","fastq","sra","ena","geo","download","synapse"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/fetchngs is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO ids (see usage docs). Usage [!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data. First, prepare a samplesheet with your input data that looks as follows: ids.csv : Each line represents a database id. Please see next section for supported ids. Now, you can run the pipeline using: [!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters ; see docs. For more details and further functionality, please refer to the usage documentation and the parameter documentation. Supported ids Via a single file of ids, provided one-per-line (see example input file) the pipeline performs the following steps: SRA / ENA / DDBJ / GEO ids 1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the ENA API 2. Fetch extensive id metadata via ENA API 3. Download FastQ files: - If direct download links are available from the ENA API: - Fetch in parallel via wget and perform md5sum check ( --download method ftp ; default). - Fetch in parallel via aspera-cli and perform md5sum check. Use --","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/fetchngs/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}