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GRAPE v1.7 Release #91

Merged
merged 72 commits into from
Jan 13, 2023
Merged

GRAPE v1.7 Release #91

merged 72 commits into from
Jan 13, 2023

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Jahysama
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@Jahysama Jahysama commented Jan 12, 2023 •
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GRAPE v1.7

Added

  • All conda environments are now built in Dockerfile and Snakemake doesn't need to create them for every workflow run from .yaml files.
  • Multiple tests were added, covering all GRAPE flows. Test cases are stored at grape/test-cases.

Changed

  • Phased affymetrix chip is now stored within the bundle to speed up the simulation flow, because of this intersect rule in pedsim simulation workflow was moved to reference downloading workflow.

Fixed

  • Fixed ibis detecting empty IBD segments causing pipeline teardown.

josephkott and others added 30 commits May 25, 2022 14:52
@josephkott
Merge pull request #73 from genxnetwork/master
892fca1 
Merge `master` to `develop`
@Jahysama
[GRAPE-126] Added creation of an empty output and empty ibd chunks lo…
8b42a94 
…gging
@Jahysama
[GRAPE-126] Fixed ersa and germline falling when empty ibd
c13854b
@Jahysama
[GRAPE-126] Added chunk number in logging
b68e8ba
@josephkott
[GRAPE-114] Pytest with GitHub actions (#74)
869b1ae
@Jahysama
edited empty output file creation
cc63bea
@Jahysama
edited chunks logging
19624d0
@Jahysama @josephkott
[GRAPE-126] Changed logging of empty ibd
11b0158 
Co-authored-by: Misha Lebedev <[email protected]>
@Jahysama
Merge pull request #75 from genxnetwork/GRAPE-126-ignore-empty-ibis-o…
509abc5 
…utput-when-no-relatives-found

[GRAPE-126] Ignore empty IBIS output when no relatives found
@josephkott
[GRAPE-114] run pytest only for develop -> master PR, forks do not ru…
4549373 
…n pytest as well (#76)
@Jahysama
added phased reference dir path
8df3147
@Jahysama
[GRAPE-127] Moved rule intersec to reference downloading
6fb6ef5
@Jahysama
[GRAPE-127] Moved rule intersec from pedsim workflow
3151aac
@Jahysama
[GRAPE-127]does not work without 'True'
428adbd
@Jahysama
added phased_vcf in rule all, unpacked ref_test inside archive
b46693c
@Jahysama
[GRAPE-127] edited new bundle link, md5, file_size
6dd75d7
@Jahysama
Merge branch 'develop' into GRAPE-127-store-phased-affymetrix-chip-da…
6153f65 
…ta-within-the-reference-bundle
@Jahysama
[GRAPE-127] Fixed bundle archive issue
5cb7d35
@Jahysama
[GRAPE-127] Added space
9b339b7
@Jahysama
[GRAPE-127] Added 2 more spaces for intent
d1b408b
@Jahysama
Merge pull request #77 from genxnetwork/GRAPE-127-store-phased-affyme…
66cab10 
…trix-chip-data-within-the-reference-bundle

[Grape-127] Store phased affymetrix chip data within the reference bundle
@Jahysama
[GRAPE-125] Added ibis-king, king-germline, aadr and khazar test cases
8d78990
@Jahysama
[GRAPE-125] Renamed ref and home dir back
2d887d4
@Jahysama
[GRAPE-119] Made plink files merge before mapping
f2d2705
@Jahysama
[GRAPE-125] Renamed vars for a better fit
6705bee
@Jahysama
Merge pull request #79 from genxnetwork/GRAPE-119-remove-rule-remove-…
9089326 
…mapping-from-rules-preprocessing-smk

[GRAPE-119] Remove rule remove mapping from rules preprocessing smk
@Jahysama
[GRAPE-125] Added test data downloading, removed _get functions
f1eb9bb
@Jahysama
[GRAPE-125] Info needed for test data downloading
9d10b6f
@Jahysama
[GRAPE-125] Made separate test from test_simulate and test_real_data
b6a77cf
@Jahysama
Merge branch 'develop' into GRAPE-125-create-automatic-tests-for-all-…
c49ec9d 
…grape-test-cases
Jahysama and others added 17 commits November 18, 2022 13:50
@Jahysama
[GRAPE-128] Added custom snakemake package
dbcdb6f
@Jahysama
[GRAPE-128] Added comment about custom snakemake
99e0645
@Jahysama
Merge branch 'develop' into GRAPE-128-pre-creation-of-conda-environme…
81700f3 
…nts-during-the-grape-docker-container-build
@Jahysama
Merge pull request #82 from genxnetwork/GRAPE-128-pre-creation-of-con…
764397d 
…da-environments-during-the-grape-docker-container-build

[GRAPE-128] Pre creation of conda environments during the grape docker container build
@Jahysama
[GRAPE-133] Added mmh3 package
8206e7a
@Jahysama
[GRAPE-134] Added update get-apt
9f6f642
@Jahysama
Merge pull request #85 from genxnetwork/GRAPE-134-docker-container-bu…
f9178f1 
…ilding-bug

[GRAPE-134] Docker container building bug
@Jahysama
[GRAPE-133] Renamed env to match in snakemake rules
c35a3da
@Jahysama
Merge pull request #84 from genxnetwork/GRAPE-133-evaluation-env-mmh-…
a74debc 
…3-bug

[GRAPE-133] Evaluation env mmh 3 bug
@Jahysama
[GRAPE-135] Executing pytest with sudo
d847b8a
@Jahysama
[GRAPE-135] Updated token
1dbf45e
@Jahysama
[GRAPE-137] Added v1.7 release notes
4f03ad4
@Jahysama
Merge pull request #87 from genxnetwork/GRAPE-137-prepare-grape-release
b4fa140 
[GRAPE-137] Prepare GRAPE release
@Jahysama
[GRAPE-135] Added numpy version (float error)
0ddcf11
@Jahysama
[GRAPE-135] pytest is now runs as root on host by default
464ebd1
@Jahysama
Merge pull request #86 from genxnetwork/GRAPE-135-docker-as-root-exec…
8f16591 
…ution-during-pytest

[GRAPE-135] Docker as root execution during pytest
@Jahysama
Merge branch 'master' into develop
80ca645
@Jahysama Jahysama closed this Jan 12, 2023
@Jahysama Jahysama reopened this Jan 12, 2023
@Jahysama Jahysama changed the title Release v1.7 GRAPE v1.7 Release Jan 12, 2023
@Jahysama Jahysama closed this Jan 12, 2023
@Jahysama Jahysama reopened this Jan 12, 2023
@Jahysama Jahysama closed this Jan 12, 2023
@Jahysama Jahysama reopened this Jan 12, 2023
@Jahysama Jahysama merged commit cce7e42 into master Jan 13, 2023
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2 participants
@Jahysama @josephkott