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Add RNABloom as assembly tool option #2

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Add RNABloom as assembly tool option #2

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d6b43c4
Add coverage and identity constraints for GMAP
ClaraUktar Jun 2, 2024
37f95ee
Fix error when no GMAP alignments
ClaraUktar Jun 23, 2024
d87a687
Update gmap for mac os
ClaraUktar Jun 23, 2024
f3be503
Update gmap for linux
ClaraUktar Jul 2, 2024
ac20ac1
Handle antisense direction during gtf creation
ClaraUktar Aug 19, 2024
7b9e8f8
WIP: Cut out contig parts based on alignment
ClaraUktar Aug 29, 2024
5364bdc
Rewrite CDS features based on exons
ClaraUktar Sep 12, 2024
2f4e2be
Sort exons before rewrite to gtf
ClaraUktar Sep 20, 2024
223bfc2
WIP: Handle indels in alignment results
ClaraUktar Apr 5, 2025
63a31ed
Exclude alignments with indels if parameter active
ClaraUktar Apr 6, 2025
0e15e84
Update MacOS environment to include RNABloom
ClaraUktar Apr 6, 2025
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8 changes: 4 additions & 4 deletions environment_linux.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -56,9 +56,9 @@ dependencies:
- bwidget=1.9.14
- bzip2=1.0.8
- c-ares=1.24.0
- ca-certificates=2023.11.17
- ca-certificates=2024.6.2
- cairo=1.16.0
- certifi=2023.11.17
- certifi=2024.6.2
- charset-normalizer=3.3.2
- click=8.1.7
- contourpy=1.1.1
Expand All @@ -82,7 +82,7 @@ dependencies:
- gfortran_impl_linux-64=13.2.0
- giflib=5.2.1
- glpk=5.0
- gmap=2023.10.10
- gmap=2024.05.20
- gmp=6.3.0
- graphite2=1.3.13
- gsl=2.7
Expand Down Expand Up @@ -155,7 +155,7 @@ dependencies:
- numpy=1.24.4
- openjdk=17.0.3
- openjpeg=2.5.0
- openssl=3.2.0
- openssl=3.3.1
- packaging=23.2
- pandas=2.0.3
- pandoc=3.1.3
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