Code

V0.10.0 dev#93

Code

Merged

kopardev merged 43 commits intomasterCCBR/CHARLIE:masterfrom v0.10.0-devCCBR/CHARLIE:v0.10.0-devCopy head branch name to clipboardDec 23, 2023

+3,288-1,377

Commits

Commits on Apr 27, 2023

• Merge branch 'release/0.9.0' into activeDev

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  19d1d16

• find_circ params parsed from config

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  811b841

Commits on May 11, 2023

• adding "touch" mode to charlie wrapper:

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  6087c10

• adding HQ related config variables

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  59be387

• adding HQ related code

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  f3f7f18

Commits on May 12, 2023

• updates to spit out 2 new versions of linear and spliced files

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  a38c348

• Merge pull request #87 from CCBR/issue85

  Show description for 752ac52
  kopardev

  authored
  752ac52

• Merge branch 'activeDev' of https://github.com/kopardev/circRNA into activeDev

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  33d40ab

• updates

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  3aff1ba

• Merge branch 'activeDev' of https://github.com/kopardev/circRNA into activeDev

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• Merge branch 'feature/findcirc_param_optimization' of https://github.com/kopardev/circRNA into activeDev

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  977cbff

Commits on May 17, 2023

• adding python37 to env for create_index or else it errors out with ModuleNotFoundError: No module named 'pandas'

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  d7fddd3

• changing minreadcount to 3

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  04b8826

• accounting for case of no virus selected... eg. sampleset 13

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  3022e6f

• bug fixes

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  e569c2c

Commits on May 18, 2023

• updated linear_bam script

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  5ea4fde

• changes to rule create_circExplorer_linear_spliced_bams to accomodate the new script

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  6410998

• adding quotes around , and as they can be empty strings

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  8dec5f9

• more bug fixes

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  e158ac7

Commits on May 24, 2023

• find_circ needs python2.7

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  3565dac

Commits on May 30, 2023

• python27 was required for find_circ_align ... replacing zcat with pigz due to trailing garbage ignored error

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  cb7b002

Commits on May 31, 2023

• escape tab and newline in rule circrnafinder

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  7851cc5

Commits on Jun 13, 2023

• circExplorer fix for #88

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  7f2d0f1

Commits on Jun 19, 2023

• adding separate "trigger" option to restart snakemake accordingly

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  5766bb5

• circExplorer strand related updates/scripts/etc

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  bff677f

• collapse find_circ parallel jobs into 1

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  b3d2124

• reverse complement flanking sequence for antisense BSJs

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  241bc73

• adding create_hq_bams rule

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  9dc2d91

• hq_bams to input

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  258fa01

Commits on Aug 14, 2023

• fix: finger does not work any more ... replacing it by lslogins to get full user information

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  6261f6d

• refactor: generalized to work with finger and lslogins

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  5887792

• refactor: updating bedtools and ucsc versions in tool.yaml

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  f6e07e7

• refactor: adding {sample}.rid2jid.tsv.gz to output files list

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  d9998df

• feature: circRNA id is independent of strand, counts for both + and - strand are reported together, strand from all callers are reported, both + and - flanking sites are reported, rev-comp function…

  Show description for 778913c
  kopardev

  committed
  778913c

Commits on Dec 18, 2023

• docs: update to README

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  2dd0fe1

• docs: update to README

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  b2cf2f0

Commits on Dec 23, 2023

• feat: adding expected output files

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  90b529a

• bugfix: findcirc can be also set to false in config.yaml

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  a74fc2e

• refactor: updating tool versions based on BIOWULF availability

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  25f7b13

• refactor: run_findcirc set to false as default

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  a8f7f2e

• chore: version update

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  aaed8ad

• chore: updating documentation

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  a8105d6

• refactor: updating link

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  ea537d2