Introduction

nf-core/seqsubmit is a bioinformatics pipeline that submits data to public archives such as ENA

Pipeline will have several modes

• mags for MAGs submission with genome_submitter wf
• bins for bins submission with genome_submitter wf
• assemblies for assembly submission with assembly_submitter wf

Requirements

• Webin account registered https://www.ebi.ac.uk/ena/submit/webin/login
• Raw reads submitted into INSDC

Setup your environment secrets before running the pipeline:

nextflow secrets set WEBIN_ACCOUNT "Webin-XXX"

nextflow secrets set WEBIN_PASSWORD "XXX"

Make sure you update with your authorised credentials.

genome_submitter

Workflow to submit MAGs and/or bins to ENA.

It takes input samplesheet.csv with fields required for genome_uploader. Fields described in docs. For now workflow converts CSV into required TSV.

Future implementation will consider missing fields (for example completeness and contamination) and would run steps to fill in the gaps.

2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))

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.

Now, you can run the pipeline using:

nextflow run nf-core/seqsubmit \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

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.

Credits

nf-core/seqsubmit was originally written by Martin Beracochea, Ekaterina Sakharova, Sofiia Ochkalova, Evangelos Karatzas.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #seqsubmit channel (you can join with this invite).

Citations

If you use this pipeline please make sure to cite all used software. This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

MGnify: the microbiome sequence data analysis resource in 2023

Richardson L, Allen B, Baldi G, Beracochea M, Bileschi ML, Burdett T, et al.

Vol. 51, Nucleic Acids Research. Oxford University Press (OUP); 2022. p. D753–9. Available from: http://dx.doi.org/10.1093/nar/gkac1080

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.