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V0.10.0 dev #93

Merged
merged 43 commits into from
Dec 23, 2023
Merged

V0.10.0 dev #93

merged 43 commits into from
Dec 23, 2023

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kopardev
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  • update documentation
  • meet requirements from journal

kopardev and others added 30 commits April 27, 2023 12:42
@kopardev
Merge branch 'release/0.9.0' into activeDev
19d1d16
@kopardev
find_circ params parsed from config
811b841
@kopardev
adding "touch" mode to charlie wrapper:
6087c10
@kopardev
adding HQ related config variables
59be387
@kopardev
adding HQ related code
f3f7f18
@kopardev
updates to spit out 2 new versions of linear and spliced files
a38c348
@kopardev
Merge pull request #87 from CCBR/issue85
752ac52 
Issue85
@kopardev
Merge branch 'activeDev' of https://github.com/kopardev/circRNA into …
33d40ab 
…activeDev
@kopardev
updates
3aff1ba
@kopardev
Merge branch 'activeDev' of https://github.com/kopardev/circRNA into …
eb19f26 
…activeDev
@kopardev
Merge branch 'feature/findcirc_param_optimization' of https://github.…
977cbff 
…com/kopardev/circRNA into activeDev
@kopardev
adding python37 to env for create_index or else it errors out with Mo…
d7fddd3 
…duleNotFoundError: No module named 'pandas'
@kopardev
changing minreadcount to 3
04b8826
@kopardev
accounting for case of no virus selected... eg. sampleset 13
3022e6f
@kopardev
bug fixes
e569c2c
@kopardev
updated linear_bam script
5ea4fde
@kopardev
changes to rule create_circExplorer_linear_spliced_bams to accomodate…
6410998 
… the new script
@kopardev
adding quotes around , and as they can be empty strings
8dec5f9
@kopardev
more bug fixes
e158ac7
@kopardev
find_circ needs python2.7
3565dac
@kopardev
python27 was required for find_circ_align ... replacing zcat with pig…
cb7b002 
…z due to trailing garbage ignored error
@kopardev
escape tab and newline in rule circrnafinder
7851cc5
@kopardev
circExplorer fix for #88
7f2d0f1
@kopardev
adding separate "trigger" option to restart snakemake accordingly
5766bb5
@kopardev
circExplorer strand related updates/scripts/etc
bff677f
@kopardev
collapse find_circ parallel jobs into 1
b3d2124
@kopardev
reverse complement flanking sequence for antisense BSJs
241bc73
@kopardev
adding create_hq_bams rule
9dc2d91
@kopardev
hq_bams to input
258fa01
@kopardev
fix: finger does not work any more ... replacing it by lslogins to ge…
6261f6d 
…t full user information
kopardev added 13 commits August 14, 2023 17:20
@kopardev
refactor: generalized to work with finger and lslogins
5887792
@kopardev
refactor: updating bedtools and ucsc versions in tool.yaml
f6e07e7
@kopardev
refactor: adding {sample}.rid2jid.tsv.gz to output files list
d9998df
@kopardev
feature: circRNA id is independent of strand, counts for both + and -…
778913c 
… strand are reported together, strand from all callers are reported, both + and - flanking sites are reported, rev-comp function updated
@kopardev
docs: update to README
2dd0fe1
@kopardev
docs: update to README
b2cf2f0
@kopardev
feat: adding expected output files
90b529a
@kopardev
bugfix: findcirc can be also set to false in config.yaml
a74fc2e
@kopardev
refactor: updating tool versions based on BIOWULF availability
25f7b13
@kopardev
refactor: run_findcirc set to false as default
a8f7f2e
@kopardev
chore: version update
aaed8ad
@kopardev
chore: updating documentation
a8105d6
@kopardev
refactor: updating link
ea537d2
@kopardev kopardev merged commit 6b03415 into master Dec 23, 2023
0 of 2 checks passed
@kopardev kopardev deleted the v0.10.0-dev branch December 23, 2023 19:32
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@kopardev