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Add profile for ARM compatibility #1425

Merged
merged 49 commits into from
Oct 23, 2024
Merged

Add profile for ARM compatibility #1425

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d59ecf7
appy changes for ARM
pabloaledo May 16, 2024
991637c
Merge branch 'arm_3.16.1' into dev
pinin4fjords Oct 17, 2024
4bdae48
Fix up config
pinin4fjords Oct 17, 2024
c9d616b
Reset environment ymls
pinin4fjords Oct 17, 2024
9f640ab
Reset main.nfs with software changes only
pinin4fjords Oct 17, 2024
00cff4c
Link sw configs to arm profile
pinin4fjords Oct 17, 2024
f281e0b
Add process block
pinin4fjords Oct 17, 2024
f5208dd
note pins
pinin4fjords Oct 17, 2024
ea8b9e8
Remove conda overrides that were having no impact
pinin4fjords Oct 17, 2024
db02d99
Use different RSEQC pin
pinin4fjords Oct 18, 2024
4a8ed2b
update BEDGRAPHTOBIGWIG pin
pinin4fjords Oct 18, 2024
b86a6f9
Fix annotation
pinin4fjords Oct 18, 2024
1b96eb8
Don't think we need the RSEQC pin
pinin4fjords Oct 18, 2024
4e5d7a3
correct ucsc
pinin4fjords Oct 18, 2024
bbd3452
Merge pull request #1 from pinin4fjords/sw_to_conf
pabloaledo Oct 18, 2024
902367e
Triage arm deps
pinin4fjords Oct 18, 2024
328d02d
Non-igenomes STAR can use the latest star
pinin4fjords Oct 18, 2024
2f92bfc
remove rogue comment
pinin4fjords Oct 18, 2024
0a563dc
update arm conf
pinin4fjords Oct 21, 2024
0be2d6a
Cut out module redundant software overrides
pinin4fjords Oct 22, 2024
bba6b92
Merge pull request #2 from pinin4fjords/triage_arm
pabloaledo Oct 22, 2024
56f1a47
Merge pull request #1414 from pabloaledo/dev
pinin4fjords Oct 22, 2024
a5e831f
Merge branch 'dev' into arm_3.16.1
pinin4fjords Oct 22, 2024
ed026be
Add frozen ARM builds
pinin4fjords Oct 22, 2024
a8d514f
Container directives for conda overrides
pinin4fjords Oct 22, 2024
8e14711
Temporary Trimgalore override, singularity fixes for rsem processes
pinin4fjords Oct 22, 2024
161cf95
update docs
pinin4fjords Oct 22, 2024
caad7fa
Fix argument conflict between STAR versions
pinin4fjords Oct 22, 2024
cdfb98b
Fix config error
pinin4fjords Oct 22, 2024
524e19e
Correction to star rsem
pinin4fjords Oct 22, 2024
7448aed
Merge branch 'arm_3.16.1' of github.com:nf-core/rnaseq into arm_3.16.1
pinin4fjords Oct 22, 2024
4f8de94
Refine config setup
pinin4fjords Oct 22, 2024
a1d558e
Bump trimgalore module
pinin4fjords Oct 22, 2024
dae2899
Fix up ARM profile for updated trim-galore
pinin4fjords Oct 22, 2024
d3580a4
Apply suggestions from code review
pinin4fjords Oct 23, 2024
32f7d32
Apply suggestions from code review
pinin4fjords Oct 23, 2024
7df162f
Add notes for kraken2/ braken
pinin4fjords Oct 23, 2024
642d2a8
Update docs
pinin4fjords Oct 23, 2024
d9e534d
prettier
pinin4fjords Oct 23, 2024
d4fcb56
lint fix
pinin4fjords Oct 23, 2024
896dd74
[skip ci] Reorg ARM bits
pinin4fjords Oct 23, 2024
314ea85
Update arm.config
drpatelh Oct 23, 2024
251481f
Fix syntax error
pinin4fjords Oct 23, 2024
cde5fef
Merge branch 'arm_3.16.1' of github.com:nf-core/rnaseq into arm_3.16.1
pinin4fjords Oct 23, 2024
f59132a
revert trimgalore tweak to appease linter
pinin4fjords Oct 23, 2024
40f05c5
Update pipeline-level tests
pinin4fjords Oct 23, 2024
2156f5d
Merge branch 'arm_3.16.1' of https://github.com/nf-core/rnaseq into a…
pinin4fjords Oct 23, 2024
79370d3
Update CHANGELOG
pinin4fjords Oct 23, 2024
424137a
Merge branch 'arm_3.16.1' of github.com:nf-core/rnaseq into arm_3.16.1
pinin4fjords Oct 23, 2024
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