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Improve reproducibility with Conda #1565

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Merged
pinin4fjords merged 19 commits into from
Jun 9, 2025
Merged

Improve reproducibility with Conda #1565

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85badf0
try to fix perl version mis-reporting
pinin4fjords Jun 6, 2025
9821ac0
Merge branch 'dev' into pin_gtf2bed_perl
pinin4fjords Jun 6, 2025
817cb19
poke ci
pinin4fjords Jun 6, 2025
c8a53f6
Merge branch 'pin_gtf2bed_perl' of github.com:nf-core/rnaseq into pin…
pinin4fjords Jun 6, 2025
20ebb74
Temporarily enable conda on dev
pinin4fjords Jun 6, 2025
f97aebc
Exclude R_sessionInfo.log from snaps
pinin4fjords Jun 6, 2025
fe36959
Properly pin for deseq2_qc
pinin4fjords Jun 6, 2025
cf79864
Poke ci
pinin4fjords Jun 6, 2025
2de1c1d
Remove some things from snapshots
pinin4fjords Jun 6, 2025
0290591
Merge branch 'pin_gtf2bed_perl' of https://github.com/nf-core/rnaseq …
pinin4fjords Jun 6, 2025
fc793a0
Try agressive pinning for umitools for conda reproducibility
pinin4fjords Jun 6, 2025
b374c9b
Use nft-bam
pinin4fjords Jun 6, 2025
75928d8
increase shards
pinin4fjords Jun 9, 2025
e21abe5
Bump ci
pinin4fjords Jun 9, 2025
9e66120
Patch umitools/dedup for stricter deps
pinin4fjords Jun 9, 2025
c24cae4
add missing umitools patches
pinin4fjords Jun 9, 2025
efc3730
update changelog
pinin4fjords Jun 9, 2025
073a387
Prettier
pinin4fjords Jun 9, 2025
ed0602f
reset CI to how it should be
pinin4fjords Jun 9, 2025
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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -8,7 +8,7 @@
"bbmap/bbsplit": {
"branch": "master",
"git_sha": "8864afe586537bf562eac7b83349c26207f3cb4d",
"installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
"installed_by": ["fastq_qc_trim_filter_setstrandedness","modules"]
},
"bedtools/genomecov": {
"branch": "master",
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2 changes: 1 addition & 1 deletion modules/local/gtf2bed/environment.yml
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Expand Up @@ -2,4 +2,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- conda-forge::perl>=5.26.2
- conda-forge::perl=5.26.2
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