Commits · devel · hem / hamlet

21 Nov, 2022 1 commit
- Update fusioncatcher to latest version · 7008095b
  van den Berg authored Nov 21, 2022
  
  7008095b
18 Nov, 2022 7 commits
- Update special chromosomes to exclude · cb1bcf98
  van den Berg authored Nov 18, 2022
  
  cb1bcf98
- Enable HGVS annotations · 3a10305e
  van den Berg authored Nov 18, 2022
  
  3a10305e
- Use a single gtf file · 89775b1b
  van den Berg authored Nov 18, 2022
  
  89775b1b
- Remove unused input fasta_vep · a182e989
  van den Berg authored Nov 18, 2022
  
  a182e989
- Remove amplicon bedfile · 144c2823
  van den Berg authored Nov 18, 2022
  
  144c2823
- Fix incorrect variant plot location · 245be935
  van den Berg authored Nov 18, 2022
  
  245be935
- Remove expression module · 05f00633
  van den Berg authored Nov 18, 2022
  
  05f00633
17 Nov, 2022 3 commits
- Download fusion datafiles · c1a7f421
  van den Berg authored Nov 17, 2022
  
  c1a7f421
- Add fasta files for flt3 and kmt2a · 7f693c95
  van den Berg authored Nov 17, 2022
  
  7f693c95
- Add small files directly and copy them · 19154ac3
  van den Berg authored Nov 17, 2022
  
  19154ac3
16 Nov, 2022 1 commit
- Don't run snakefmt on the utilities · dd760ebe
  van den Berg authored Nov 16, 2022
  
  dd760ebe
15 Nov, 2022 2 commits
- Unpack vep cache · 29b21c24
  van den Berg authored Nov 15, 2022
  
  29b21c24
- Download vep cache database · c20fa637
  van den Berg authored Nov 15, 2022
  
  c20fa637
14 Nov, 2022 1 commit
- Add genome hotspots · bf0a05a9
  van den Berg authored Nov 14, 2022
  
  bf0a05a9
08 Nov, 2022 1 commit
- Revert "Workaround: Use python 3.10 or lower" · 1816aae8
  van den Berg authored Nov 08, 2022
```
This reverts commit 5aa03630.
```
  1816aae8
07 Nov, 2022 3 commits
- Workaround: Use python 3.10 or lower · 5aa03630
  van den Berg authored Nov 07, 2022
```
See https://github.com/snakemake/snakemake/issues/1952
```
  5aa03630
- Use fewer containers · 86fafcc7
  van den Berg authored Nov 07, 2022
  
  86fafcc7
- Update fsnviz to work with latest version of star-fusion · cb19ee79
  van den Berg authored Nov 07, 2022
  
  cb19ee79
31 Oct, 2022 1 commit
- Remove hardcoded containers · 15c9de8b
  van den Berg authored Oct 31, 2022
  
  15c9de8b
28 Oct, 2022 3 commits
- Remove all dependencies on click · f4d5812f
  van den Berg authored Oct 28, 2022
  
  f4d5812f
- Use json module_output for itd · 0891fbe7
  van den Berg authored Oct 28, 2022
  
  0891fbe7
- Remove click, simplify code · 30d541da
  van den Berg authored Oct 28, 2022
  
  30d541da
27 Oct, 2022 17 commits
- snkfmt · 56e3c719
  van den Berg authored Oct 27, 2022
  
  56e3c719
- Add module_output to itd module · d077428b
  van den Berg authored Oct 27, 2022
  
  d077428b
- Add json output to itd module · 571fe41a
  van den Berg authored Oct 27, 2022
  
  571fe41a
- Add module_output to snv-indels module · b4e9d2f3
  van den Berg authored Oct 27, 2022
  
  b4e9d2f3
- Add output schema for snv-indels module · f23c69db
  van den Berg authored Oct 27, 2022
  
  f23c69db
- Use snv-indels module json file in summary · f2142c37
  van den Berg authored Oct 27, 2022
  
  f2142c37
- Add json output file to snv-indels module · e7c4f33d
  van den Berg authored Oct 27, 2022
  
  e7c4f33d
- Refactor fusion outputs · d4971ae9
  van den Berg authored Oct 27, 2022
  
  d4971ae9
- Add explicition optional module output · 52dd2eb0
  van den Berg authored Oct 26, 2022
  
  52dd2eb0
- Deprecate svg figures · 931d4887
  van den Berg authored Oct 26, 2022
  
  931d4887
- Refactor fusion json to use explicit inputs · 0d675dab
  van den Berg authored Oct 26, 2022
  
  0d675dab
- Add test for star-fusion only output (no intersection) · d4daffb0
  van den Berg authored Oct 26, 2022
  
  d4daffb0
- Only name and sf_count are required for fusion events · 016db718
  van den Berg authored Oct 26, 2022
  
  016db718
- Parse star fusion results with crimson · e0800730
  van den Berg authored Oct 21, 2022
  
  e0800730
- Pass appropriate files directly · 533ac643
  van den Berg authored Oct 21, 2022
```
Instead of globbing around in the fusing folder and pulling out stuff we
need.
```
  533ac643
- Add tests for fusion png plots · 8878b3e0
  van den Berg authored Oct 21, 2022
  
  8878b3e0
- Add additional tests for the fusion json output · 4eb7ac6b
  van den Berg authored Oct 21, 2022
  
  4eb7ac6b