{"repo":"nf-core/seqsubmit","free":true,"listed":false,"github":"https://github.com/nf-core/seqsubmit","clone":"git clone https://github.com/nf-core/seqsubmit.git","description":"nf-core pipeline for data submission to ENA","language":"Nextflow","stars":18,"topics":["nextflow","nf-core","pipeline","workflow"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/seqsubmit is a Nextflow pipeline for submitting sequence data to ENA. The pipeline currently supports the following submission modes, each routed to a dedicated workflow: - reads — raw sequencing reads submission via the READSUBMIT workflow ( pink ) - metagenomic assemblies — assembly submission via the ASSEMBLYSUBMIT workflow ( green ) - mags — metagenome-assembled genomes (MAGs) submission via the GENOMESUBMIT workflow ( blue ) - bins — bins submission via the GENOMESUBMIT workflow ( blue ) Each workflow has its own samplesheet structure, prerequisites, and limitations — they are briefly described below. See the usage documentation for more detailed explanations. Requirements - Nextflow =25.04.0 - A Webin account registered at Set your Webin credentials as Nextflow secrets: Make sure to replace the values above with your own credentials. - Provide either a study accession or a study registration metadata file for the study the submission will be associated with. See the Submission study section of the usage documentation for details. - Depending on the chosen mode, samples, reads, or metagenomic assemblies must be pre-submitted to ENA to obtain the corresponding accessions, which you then reference in your submission. Refer to the relevant mode section in the usage documentation for details. Input samplesheets reads mode Example: See the reads mode section of the usage documentation for more details. metagenomic assemblies mode Example: See the metageno","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/seqsubmit/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."}