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elan-2.0.0
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Inbound Data Operations Badge

Elan

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

go-full-elan.sh

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
MQTT_ENV Root MQTT topic (CLIMBDEV or COGUK)
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

go-full-elan.sh will immediately terminate with exit 64 (EX_USAGE) if any of the listed parameters are missing from the environment.

cog-publish.sh

Note these variables are checked inside go-full-elan.sh as it is the main entrypoint. Additionally, variables defined above may be used in cog-publish.sh 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 https://www.nextflow.io/docs/latest/config.html

Invocation

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/go-full-elan.sh $DATESTAMP

Etymology

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.

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