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Inbound Data Operations Badge


Elan is the inbound distribution pipeline for CLIMB-COVID. Elan is a Nextflow DSL2 pipeline for quality checking dispersed files and publishing them to a common location.

Elan was authored by @samstudio8 as part of CLIMB-COVID's work with the COVID-19 Genomics UK Consortium. Elan is now maintained by @BioWilko.

Parameters and environment variables

Controlling Elan

Name Description
DATESTAMP YYYYMMDD datestamp to identify today's run
UPLOADS_DIR_GLOB Uploads glob to expand as part of resolve_uploads
ELAN_CONFIG Path to current Nextflow configuration
ELAN_SOFTWARE_DIR Path to local clone of elan-nextflow
ELAN_RUN_DIR Path to dir to run Elan from (scratch)
ELAN_DIR Path to CLIMB-COVID staged artifacts root (nicholsz/), passed as --publish to elan-nf
ARTIFACTS_ROOT Path to new CLIMB-COVID published artifact root (/artifacts/), passed as --artifacts_root to elan-nf
NEXTFLOW_BIN Path to nextflow binary
SLACK_MGMT_HOOK Slack HTTPS webhook for posting debug messages
SLACK_REAL_HOOK Slack HTTPS webhook for posting inbound-dist messages
MQTT_HOST IP for MQTT broker
CONDA_OCARINA conda prefix to conda activate when performing ocarina calls outside of Elan
CONDA_IPC conda prefix to conda activate when sending MQTT messages with Tael will immediately terminate with exit 64 (EX_USAGE) if any of the listed parameters are missing from the environment.

Note these variables are checked inside as it is the main entrypoint. Additionally, variables defined above may be used in without listing them below.

Name Description
COG_PUBLISH_MODE Set to local or slurm to control how the daily consensus is generated
CONDA_POSTELAN conda prefix to conda activate for publish related activities

Running Elan

elan-nextflow parameters

Name Description
--mode inbound or ocarina
--ocarina_profile Ocarina profile to use for save_manifest (inbound) or play_ocarina (ocarina)
--datestamp (elan) YYYYMMDD datestamp to identify today's run
--uploads (elan) Glob path for CLIMB-COVID user uploads (ensure to quote appropriately to prevent premature glob expansion)
--publish (elan) Path to CLIMB-COVID staged artifacts root (nicholsz/)
--artifacts_root (elan) Path to new CLIMB-COVID published artifact root (/artifacts/)
--minlen (elan) Minimum genome size required to pass the screen_uploads step [int]
--manifest (ocarina) Path to Ocarina manifest created by Elan pipeline

elan-nextflow environment variables

Name Description
ELAN_SLACK_MGMT_HOOK HTTPS hook for posting management and control messages to Slack
ELAN_SLACK_INBOUND_HOOK HTTPS hook for posting counts and QC messages to Slack
OCARINA_CONF_FILE Path to Ocarina JSON configuration
OCARINA_PROFILE Profile to load from Ocarina JSON configuration

Note that Elan will only error if MAJORA_DOMAIN is unset, all other MAJORA_* variables are not checked.

Nextflow environment variables

Name Description
NXF_WORK Path to NXF working dir (basename must be nxf_work on CLIMB-COVID)
NXF_CONDA_CACHEDIR Path to conda cache dir (basename must be .conda on CLIMB-COVID)
NXF_DEBUG One of: 1,2,3. See


Add the following line to the execution node's crontab:

1 4 * * * export EAGLEOWL_CONF=/path/to/eagle-owl/config; export DATESTAMP=`date +\%Y\%m\%d`; /path/to/elan/repo/bin/control/ $DATESTAMP


Elan is named after an aqueduct whose source is in the Elan Valley in Powys, Mid Wales. In the late 1800s, the Birmingham Corporation Water Department constructed a series of dams in the valley and an aqueduct stretching 73 miles (117 km) to carry water to Birmingham. The aqueduct served a vital supply of clean water to the West Midlands to improve public health in the region.


for data flowing to birmingham







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