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Split GISAID profile to "six-month" and "all-time" builds #910

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merged 7 commits into from
Apr 30, 2022
Merged

Split GISAID profile to "six-month" and "all-time" builds #910

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638470f
Split GISAID profile to "six-month" and "all-time" builds
trvrb Apr 30, 2022
4a35ef5
Split Nextstrain open builds to generate "6m" and "all-time" targets
trvrb Apr 30, 2022
206a97e
Increase compute resources for Nextstrain builds
trvrb Apr 30, 2022
e9ffad1
Fix parsing of build names with complex prefixes
huddlej Apr 18, 2022
bd2d766
Escape regexp metachars when using auspice_json_prefix as a wildcard …
tsibley Apr 25, 2022
b172c2a
Upload files for 6m builds to the same URLs as the previous builds
tsibley Apr 29, 2022
7bbc46e
Update change log
trvrb Apr 30, 2022
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6 changes: 3 additions & 3 deletions .github/workflows/rebuild-gisaid.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -50,14 +50,14 @@ jobs:
nextstrain build \
--aws-batch \
--detach \
--cpus 36 \
--memory 70GiB \
--cpus 72 \
--memory 140GiB \
. \
deploy \
upload \
--config "${config[@]}" \
--profile nextstrain_profiles/nextstrain-gisaid \
--set-threads tree=16 \
--set-threads tree=8 \
|& tee build-launch.log
env:
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
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6 changes: 3 additions & 3 deletions .github/workflows/rebuild-open.yml
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Expand Up @@ -51,14 +51,14 @@ jobs:
nextstrain build \
--aws-batch \
--detach \
--cpus 36 \
--memory 70GiB \
--cpus 72 \
--memory 140GiB \
. \
deploy \
upload \
--config "${config[@]}" \
--profile nextstrain_profiles/nextstrain-open \
--set-threads tree=16 \
--set-threads tree=8 \
|& tee build-launch.log
env:
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
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8 changes: 4 additions & 4 deletions defaults/parameters.yaml
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Expand Up @@ -81,8 +81,8 @@ filter:
exclude_where: "division='USA'"
exclude_ambiguous_dates_by: "any"

# Exclude sequences which are from before late 2019 (likely date mix-ups)
min_date: 2019.74
# Exclude sequences which are from before Dec 2019 (likely date mix-ups)
min_date: "2019-12-01"

# When choosing contextual samples for a focal set, applying crowding penalty
# will help reduce the number of genetically identical strains that get chosen,
Expand Down Expand Up @@ -136,10 +136,10 @@ frequencies:
# min_date is set by default to 1 year before present
# but can be explicitly set if desired

# Number of months between pivots
# Number of weeks between pivots
pivot_interval: 1

# Measure pivots in weeks rather than months
# Measure pivots in weeks
pivot_interval_units: "weeks"

# KDE bandwidths in proportion of a year to use per strain.
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2 changes: 2 additions & 0 deletions docs/src/reference/change_log.md
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Expand Up @@ -5,6 +5,8 @@ We also use this change log to document new features that maintain backward comp

## New features since last version update

- 29 April 2022: Include multiple timespans in Nextstrain profile builds. [PR 910](https://github.com/nextstrain/ncov/pull/910)

- 29 April 2022: Update default mask parameters to mask 200 bases from the end of the genome rather than the existing 50. This was necessary because there is a large deletion in this region in circulating 21L viruses. This deletion is causing problems with alignment and the resulting mis-alignment appears as excess mutations in the tree. [PR 939](https://github.com/nextstrain/ncov/pull/939).

- 27 April 2022: Include new clades 22A, 22B and 22C, where 22A corresponds to Pango lineage BA.4, 22B corresponds to Pango lineage BA.5 and 22C corresponds to Pango lineage BA.2.12.1. Please see [PR 933](https://github.com/nextstrain/ncov/pull/933) for rationale behind these clade updates.
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