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uclahs-cds
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pipeline-call-NonCanonicalPeptide
Nextflow pipeline to call non-canonical peptides as custom databases for proteogenomic analysis
https://automatic-adventure-o4l96o9.pages.github.io/
GNU General Public License v2.0
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Update moPepGen to 0.9.0
#71
zhuchcn
closed
2 years ago
0
bump mopepgen to 0.8.1
#70
lydiayliu
closed
2 years ago
0
bump moPepGen to 0.8.0
#69
lydiayliu
closed
2 years ago
0
bump MoPepGen to 0.7.2
#68
lydiayliu
closed
2 years ago
0
Update moPepGen to 0.7.1
#67
zhuchcn
closed
2 years ago
0
tweak the pipeline to have docker parameter added
#66
lydiayliu
closed
2 years ago
0
the SVG is gone??
#65
lydiayliu
closed
1 year ago
1
don't output merged peptides if filtering is required
#64
lydiayliu
closed
1 year ago
1
call-NonCanonicalPeptides
#63
zhuchcn
closed
2 years ago
0
Fixed merge workflow that splitFasta was not included
#62
zhuchcn
closed
2 years ago
14
Complex filtering
#61
lydiayliu
opened
2 years ago
1
fasta entry merge + split missing output
#60
lydiayliu
closed
2 years ago
3
Fix issue the each individual FASTA is called to merge
#59
zhuchcn
closed
2 years ago
0
Seems like `mergeFasta` is called on each individual FASTA file instead of all FASTA.. But seems like this is still node failure?
#58
zhuchcn
closed
2 years ago
0
fix typo in merge_fasta
#57
lydiayliu
closed
2 years ago
0
Ill use of parameter `combine_variant_noncoding`
#56
lydiayliu
closed
2 years ago
0
bump mpg version to 0.6.1
#55
lydiayliu
closed
2 years ago
0
mopepgen_version to '0.6.0'
#54
lydiayliu
closed
2 years ago
0
bump mpg to 0.5.1
#52
lydiayliu
closed
2 years ago
0
Add `mergeFasta` to combine variant and noncoding peptides
#51
zhuchcn
closed
2 years ago
2
A couple of things the pipeline currently cannot do
#50
lydiayliu
closed
2 years ago
5
bump mopepgen_version = '0.5.0'
#49
lydiayliu
closed
2 years ago
2
filter_fasta did not run
#48
lydiayliu
closed
2 years ago
2
bump mopepgen version to 0.4.2
#47
lydiayliu
closed
2 years ago
0
fix (summarize_fasta): --ignore-missing-source added
#46
zhuchcn
closed
2 years ago
2
add `--ignore-missing-source` to `summarizeFasta`
#45
lydiayliu
closed
2 years ago
1
bump mpg to 0.4.1
#44
lydiayliu
closed
2 years ago
0
File output file names
#43
zhuchcn
closed
2 years ago
6
mpg to 0.4.1
#42
lydiayliu
closed
2 years ago
0
filtered fastas are named twice
#41
lydiayliu
closed
2 years ago
0
Various docker: Error response from daemon
#40
lydiayliu
closed
2 years ago
1
fix (summarizeFasta): parameter namespace fixed
#39
zhuchcn
closed
2 years ago
0
How are params to `summarizeFasta` passed in?
#38
lydiayliu
closed
2 years ago
2
fixed filterFasta that it will not run if it is set to false
#37
zhuchcn
closed
2 years ago
2
separate filterFasta for noncoding and variant peptides
#36
zhuchcn
closed
2 years ago
3
summarizeFasta is called before and after running filterFasta
#35
zhuchcn
closed
2 years ago
2
Arriba and FusionCatcher output not input into callVariant
#34
zhuchcn
closed
2 years ago
2
entrypoint of variant fasta added to skip callVariant
#33
zhuchcn
closed
2 years ago
2
circRNA testing gvf file updated
#32
zhuchcn
closed
2 years ago
2
add `summarizeFasta`?
#31
lydiayliu
closed
2 years ago
0
mpg up to 0.4.0
#30
lydiayliu
closed
2 years ago
0
can `filterFasta` also filter `noncoding_peptides`
#29
lydiayliu
closed
2 years ago
9
option to turn off callVariant
#28
lydiayliu
closed
2 years ago
0
README to add
#27
lydiayliu
closed
2 years ago
2
Lyl bump mpg
#26
lydiayliu
closed
2 years ago
0
splitFasta connector `-` or `_`?
#25
lydiayliu
closed
2 years ago
2
`decoyFasta` unrecognized arguments
#24
lydiayliu
closed
2 years ago
0
Adding encodeFasta and decoyFasta
#23
zhuchcn
closed
2 years ago
2
bump moPepGen version to 0.3.0
#22
lydiayliu
closed
2 years ago
0
GVF reference_index all messed up
#21
lydiayliu
closed
2 years ago
3
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