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Make genomic FASTA input optional #1490

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merged 26 commits into from
Jan 22, 2025
+925 −332
Merged

Make genomic FASTA input optional #1490

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a69d1d2
Update salmon indexing module
pinin4fjords Jan 21, 2025
c4a416d
Make fasta optional for gtf filtering
pinin4fjords Jan 21, 2025
0723238
Allow no fasta during param checks
pinin4fjords Jan 21, 2025
7c73f77
Rework prepare_genome for optional fasta
pinin4fjords Jan 21, 2025
53a1638
Fix bbsplit param usage for optional fasta
pinin4fjords Jan 21, 2025
4bb0af1
Add test for no fasta
pinin4fjords Jan 21, 2025
64a4547
lint fix
pinin4fjords Jan 21, 2025
d6ef689
Add snap for new test
pinin4fjords Jan 21, 2025
cbd5201
Restore output comments
pinin4fjords Jan 21, 2025
47b292c
Restore input comments
pinin4fjords Jan 21, 2025
b5e676b
Restore file comment
pinin4fjords Jan 21, 2025
b622f53
Restore existence checks
pinin4fjords Jan 21, 2025
0fdf742
Remove some unecessary changes
pinin4fjords Jan 21, 2025
f139bbe
Update changelog
pinin4fjords Jan 21, 2025
a9684ea
Remove duplicate section
pinin4fjords Jan 21, 2025
35ec56c
Fix for tweaked filtered GTF name
pinin4fjords Jan 22, 2025
0d4ef8f
Fix for tweaked filtered GTF name
pinin4fjords Jan 22, 2025
ae062b9
Update docs
pinin4fjords Jan 22, 2025
efb8e07
Temporarily disable 'latest-everything' testing due to incompatibilit…
pinin4fjords Jan 22, 2025
4e2dce2
Merge branch 'optional_fasta' of https://github.com/nf-core/rnaseq in…
pinin4fjords Jan 22, 2025
445ca7d
Apply suggestions from code review
pinin4fjords Jan 22, 2025
c45fbe5
Apply suggestions from code review
pinin4fjords Jan 22, 2025
bd585b0
Fix file names in snap
pinin4fjords Jan 22, 2025
871644d
Merge branch 'optional_fasta' of https://github.com/nf-core/rnaseq in…
pinin4fjords Jan 22, 2025
f07b1b1
Update usage.md
pinin4fjords Jan 22, 2025
21eb5ad
prettier
pinin4fjords Jan 22, 2025
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Temporarily disable 'latest-everything' testing due to incompatibilit… 
…ies with nf-core
@pinin4fjords
pinin4fjords authored Jan 22, 2025
commit efb8e077ca793278aa6c6a530737663485c1933d
1 change: 0 additions & 1 deletion .github/workflows/ci.yml
View file
Original file line number Diff line number Diff line change
@@ -51,7 +51,6 @@ jobs:
matrix:
NXF_VER:
- "24.04.2"
- "latest-everything"
nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"]
profile:
- "docker"