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fix: update channel priorities and snakemake wrappers #562

Merged
merged 25 commits into from
Oct 12, 2022
Merged

fix: update channel priorities and snakemake wrappers #562

merged 25 commits into from
Oct 12, 2022

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alethomas
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@alethomas alethomas commented Sep 1, 2022 •
edited by johanneskoester
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Description

To avoid package issues, all channel priorities and snakemake wrappers should be updated

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alethomas and others added 22 commits September 1, 2022 10:24
@alethomas
change channel priorities in all environments
fa98dab
@alethomas
fix
9e237de
@alethomas
change python version
fd88949
@alethomas
fix typo
9b139d4
@alethomas
remove stage in
b3e0ecf
@alethomas
revert python version pinning
51130a1
@lenakinzel
updated versions of wrappers in rules
4b817aa
@lenakinzel
removed dependency of entrez-direct from entrez.yaml as a test becaus…
e536aae 
…e of error message
@johanneskoester
fix entrez env
ff1f184
@johanneskoester
Update bcftools concat wrapper
03e2baf
@johanneskoester
update bcftools concat wrapper
714e672
@johanneskoester
bump to latest entrez
1912a0a
@johanneskoester
fix output file names for bwa index wrappers
d4244cd
@johanneskoester
adapt sort argument of bwa mem wrapper to latest version
3926a52
@johanneskoester
adapt mark duplicates to wrapper changes
8f94494
@johanneskoester
bump pangolin
6e63980
@johanneskoester
requre older tabulate version
89ae9ba
@johanneskoester
fmt
0919bfc
@johanneskoester
try bumping notebook version
801006b
@johanneskoester
fix: notebook versions
c1d8768
@johanneskoester
fix wrapper name
dd22df0
@johanneskoester
bump bcftools concat wrapper
6ef3f50
@johanneskoester johanneskoester merged commit a0b6fd0 into master Oct 12, 2022
@johanneskoester johanneskoester deleted the fix-channel-prio branch October 12, 2022 14:07
@github-actions github-actions bot mentioned this pull request Oct 12, 2022
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@johanneskoester johanneskoester johanneskoester approved these changes

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3 participants
@alethomas @johanneskoester @lenakinzel