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elan-ena

A Nextflow pipeline for smoothly transferring fresh consensus sequences to ENA via webin-cli. This fork is maintained specifically for CLIMB-COVID assembly submissions to ENA.

Parameters

Required command line parameters

Name Description
--study ENA study identifier (PRJEB)
--manifest Assembly metadata manifest
--webin_jar Path to webin-cli JAR (releases)
--out Path to write successful accessions table

Required environment variables

Additionally, you will need to set the following parameters in your environment:

Name Description
WEBIN_USER EMBL-EBI Webin username
WEBIN_PASS EMBL-EBI Webin password

Optional command line parameters

Name Description
--ascp Enable ascp transfer with webin-cli (ascp must be on your PATH)
--test Enable webin-cli test mode
--description Template for DESCRIPTION field (supports expansion of CSV row variables)

Invocation

export WEBIN_USER='Webin-00000'
export WEBIN_PASS='hunter2'
nextflow run climb-covid/elan-ena-nextflow -r stable \
    --study PRJEB00000 \
    --manifest /path/to/manifest.tsv \
    --webin_jar /path/to/webin-cli.jar \
    --out hoot.accessions.txt \
    --ascp --test
    --description 'SAMPLE:${-> row.central_sample_id}|RUN:${-> row.run_name}'

To update a local copy:

nextflow pull climb-covid/elan-ena-nextflow