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First Release PR - Pacvar#4

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tanyasarkjain wants to merge 220 commits intomasternf-core/pacvar:masterfrom devnf-core/pacvar:devCopy head branch name to clipboard

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Commits

Commits on Sep 18, 2024

• updated configuration files

  

  Tanya Jain

  committed
  374bcb7

• changes in config to account for bam input rather than fasta input

  

  Tanya Jain

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  170da29

• lima demultiplexing added

  

  Tanya Jain

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  82d8853

Commits on Sep 19, 2024

• added new module pbmm2 (missing tests for module as of now) - added pbmm2 task

  

  Tanya Jain

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  66ae8f7

Commits on Sep 24, 2024

• adding samtools functionality

  

  Tanya Jain

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  b2993fe

Commits on Sep 25, 2024

• cleaned up samtools functionality

  

  Tanya Jain

  committed
  5a703b8

Commits on Oct 8, 2024

• some small mem changes to make compatible with docker

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  committed
  21a99f8

• adding deepvariant (though still potentially need to resolve singularity issues)

  

  Tanya Jain

  committed
  346ecc3

Commits on Oct 21, 2024

• added gatk4haplotype caller

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  committed
  48592c7

Commits on Oct 22, 2024

• Update README.md

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  authored
  d874058

• Add files via upload

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  authored
  e6415b4

• Update README.md

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  authored
  59fd18b

• Add files via upload

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  authored
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• Update README.md

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• Add files via upload

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• Update README.md

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• Update README.md

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• Update README.md

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• Update README.md

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• Update README.md

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• Update README.md

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• Add files via upload

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  9c9a89a

Commits on Oct 28, 2024

• seperate workfall for bam variant calling

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  committed
  303543e

Commits on Oct 30, 2024

• added regions to deepvariant

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  56ea0cd

• deepvariant working on savio cluster (singularity)

  

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  committed
  24aee57

Commits on Nov 1, 2024

• changes

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• change

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  646bf0a

• succ run + changing to process_high from process_large

  

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  committed
  cf172cf

Commits on Nov 5, 2024

• trgt workflow

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  committed
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• change to fasta

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• sort

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• simplified plot functionality

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• typo

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• change

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• small change

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• adding id option

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• fai

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• indexing

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• small config changes

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• config

  

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• new config for wgs

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• config update

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• slight changes

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• changes

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• test

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  28f208b

Commits on Nov 7, 2024

• changes

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• files unchanged fix

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• adding hiphase functionality

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Commits on Nov 8, 2024

• 1 failure with aws triggering

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  committed
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• Add files via upload

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  authored
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• Add files via upload

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• Update README.md

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  authored
  74b2b0a

• Update README.md

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  1f56856

• Update README.md

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• Update CITATIONS.md

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• Add files via upload

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• Update README.md

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  c0b97fe

• update

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  committed
  377cb01

• merge conflict resolution?

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• small todo resolutions

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  0c11583

• Update usage.md

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• Update usage.md

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• Update output.md

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  3e89c43

• Update README.md

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  7656221

• Update README.md

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  6f9c815

• Update pacvar.nf

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  ddbf56d

• Update output.md

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• sh be minor changes

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  committed
  1152d5a

• changing intervals

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  7bebcf7

• hopefully solved the interval issue

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  c56ebe3

• consolidate

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• seems to be working

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  7b52e42

• deleting comment

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  35c13e5

Commits on Nov 9, 2024

• delete uneeded files

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  committed
  b2d8232

Commits on Nov 10, 2024

• changes

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  committed
  046f425

Commits on Nov 11, 2024

• small changes

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  committed
  baf565c

• downgraded nf-core

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  7afee9d

• all tests passing - still need to resolve warnings

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  0057f8e

Commits on Nov 12, 2024

• resolving some errors

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  committed
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• more changes

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  committed
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• Add files via upload

  tanyasarkjain

  authored
  c843076

• Update README.md

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  223608f

• more warning resolutions

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  committed
  cb775d1

• update

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  aa1b41f

• working for all trials

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  cdfe995

• removing output files for final pipeline first release

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  9e9adce

• clean up

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  01461e7

• deleting out dir

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  d2ae46c

• Merge branch 'master' into pacvar

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  authored
  ebd8c3d

• small gatk change

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  committed
  be5aae9

• Merge branch 'pacvar' of https://github.com/tanyasarkjain/pacvar into pacvar

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  committed
  90114a6

• change in spacing

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• space change

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• space

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  2a93b73

Commits on Nov 13, 2024

• changing memory

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  38905dc

• some changes

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  95da6c8

• resetting template to 2.14.0

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  09280fc

• tryna upgrade to version 3.0.2

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  0bc903c

• Template update for nf-core/tools version 3.0.2

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  21cc9f3

• Template update for nf-core/tools version 3.0.2

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  018dda1

• passing all tests version 3.0.2 - yet to try again locally

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  93985a9

• syntax error

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• 3.0.2

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  1a0a747

• updating .nf-core.yml

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  1202756

• fixed a few upgrade to 3.0.2 issues

  

  Tanya Jain

  committed
  7e70d6b

• some corrections -- still more errors

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  5450376

• working except for the naming which is null at the moment

  

  Tanya Jain

  committed
  6ea827c

• fixed meta id issue

  

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  3785686

Commits on Nov 14, 2024

• mem test conf

  

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  committed
  8930d63

• conf changes

  

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  cae0229

• pretty, 3.02 and linted

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• no out

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  454838b

• changed nextflow.config to get rid of custom config

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  ee2309e

• increasing memory

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  924207a

• changing gB

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  430dec2

• increasing cpu further for github actions

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  0d2fe9f

• subset of the data for mem saving

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  cf4de9e

• smaller

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  41ced78

• modifying config files

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  0ce6978

• made dataset much smaller

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  278e31c

• removing test files

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  e3563d6

• updated bed

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  committed
  eb924e4

• removing gatk test and making it a full test

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  committed
  00fb5f4

• pretty

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  committed
  dc56de6

Commits on Nov 15, 2024

• hope this passes

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  committed
  76a8f2c

• some small config changes and removing print statements

  tanyasarkjain

  committed
  6e386c2

• Update README.md

  tanyasarkjain

  authored
  40f47c2

• Update README.md

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  authored
  bc0a0c8

• pretty

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  committed
  212687c

• small documentation changes

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  committed
  d093494

Commits on Nov 21, 2024

• Update README.md

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  tanyasarkjain

  and

  fellen31

  authored
  fd2ce54

• Update README.md

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  tanyasarkjain

  and

  fellen31

  authored
  b07a17a

• Update README.md

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  and

  fellen31

  authored
  4699e0b

• Update README.md

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  and

  fellen31

  authored
  5971df7

• Update assets/schema_input.json

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  and

  fellen31

  authored
  499c5fb

• resolving review comments

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  committed
  223d917

• Update docs/usage.md

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  and

  fellen31

  authored
  b9234f3

• Update docs/usage.md

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  and

  fellen31

  authored
  3b5a7d0

• resolution of more review comments

  tanyasarkjain

  committed
  0837097

• Update conf/test.config

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  and

  fellen31

  authored
  190bc77

• Update conf/test_full.config

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  and

  fellen31

  authored
  c36b60f

• Update conf/test_wgs_deepvariant.config

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  and

  fellen31

  authored
  91bc8e6

• Update nextflow.config

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  tanyasarkjain

  and

  fellen31

  authored
  af6e510

• updating the release version from 0.1.0 to 1.0.0

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  committed
  9a9999b

• Update subworkflows/local/bam_snp_variant_calling/main.nf

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  tanyasarkjain

  and

  fellen31

  authored
  fc27915

• fixing mapping error

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  committed
  23bae51

• fixing pacvar.nf include alignments

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  ed7bccf

• changing mapping

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  e4c442d

Commits on Nov 26, 2024

• changed deepvariant documentation

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• changed trgt documentation

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• pretty

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• changed nextflow schema file

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• changing tools to snv_caller

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• pretty

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• changed nextflow_config to reflect name change

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  79468c4

• changing id to repeat_id

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  70da723

• changing usage to reflect change from id to repeat_id naming?

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  4d01c39

• fixing small indent issue and also changing a residual id to a repeat_id

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  committed
  e3f87df

• small change to bring pbmm2_align outside the else statement

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  committed
  3563a07

• changed set value channel to not account for zipped files as was un-needed for this use case

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  5d6be3b

• changing pbi to no longer be required

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  c08cba2

• enforcing snv_caller to either be gatk4 or deepvariant

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  5289a27

• changed bam_snp_variant_calling to only check equal instead of contains

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• adding pbi

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  9f25386

• changing base path

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  f391f30

• made nextflow schema clearer

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  29dd20a

• fixed typo

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• adding versioning

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  b0ce95b

• restoring testdata base path to what it was

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  240dda8

• Update output.md

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  authored
  558c288

• Update output.md

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• Update output.md

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• pretty

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  committed
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• changed intervals and also removed ememoty dbsnp from test

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• pretty

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• trying to transfer to new trgt modules

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  committed
  b589037

Commits on Nov 27, 2024

• deleted local copy of trgt

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• trgt

  

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  committed
  516ef4a

• Merge pull request #7 from tanyasarkjain/dev

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  tanyasarkjain

  authored
  69d934d

• fixing plot error

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  committed
  d44c77c

• Merge branch 'dev' of https://github.com/nf-core/pacvar into dev

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  committed
  c78ae48

• changing the output prefix

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  c67843e

• removed output

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  committed
  2fcae5e

• Update README.md

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  authored
  f8cf2f5

• Add files via upload

  tanyasarkjain

  authored
  ae9fd46

• Update README.md

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  tanyasarkjain

  authored
  448fda8

• Update README.md

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  authored
  8b12a13

Commits on Nov 28, 2024

• Update docs/output.md

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  tanyasarkjain

  and

  fellen31

  authored
  56e297d

• Update conf/test_wgs_gatk.config

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  and

  fellen31

  authored
  7db788c

• Update main.nf

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  and

  fellen31

  authored
  05512eb

• Update subworkflows/local/repeat_characterization/main.nf

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  and

  fellen31

  authored
  3201ea7

• Update subworkflows/local/bam_snp_variant_calling/main.nf

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  and

  fellen31

  authored
  1dfcb2c

• Update subworkflows/local/repeat_characterization/main.nf

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  and

  fellen31

  authored
  c98da99

Commits on Nov 29, 2024

• pretty-ified

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  committed
  095a8d8

• should have resolved all the comments

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  a11dd43

• fixing typo

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• fixing 2nd typo

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• removing tumor

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Commits on Nov 30, 2024

• trying to fix the trgt plot issue

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  6557f6c

• checking what repeat values looks like

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  d7c13bc

• viewing to see what repeat form looks like

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• viewing to see what repeat form looks like

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  d7769a8

• restructuring id input

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  63e393b

• fixed language style issue

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• adding karyotyping for trgt genotype

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  17a79c7

• fixed karyotype issue

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• another typo

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• testing

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• examining karyotype

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• test

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• trying to test defualts

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• changing karyotype default

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  a12649e

• fixing the karyotype issue

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  bfd35a1

Commits on Dec 2, 2024

• updated subworkflows

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  5c92589

• restoring deepvariant

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  3f49bd9

• fixed deepvariant

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  3e0e483

Commits on Dec 5, 2024

• dev

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  c01c06a

• updated full test

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  20e90bf

Commits on Dec 6, 2024

• removing un-needed logic

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• pretty

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