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First Release PR - Pacvar #4

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First Release PR - Pacvar #4

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tanyasarkjain
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@tanyasarkjain tanyasarkjain commented Nov 15, 2024 •
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/pacvar branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

Tanya Jain and others added 30 commits September 18, 2024 12:40
updated configuration files
374bcb7
changes in config to account for bam input rather than fasta input
170da29
lima demultiplexing added
82d8853
added new module pbmm2 (missing tests for module as of now) - added p…
66ae8f7 
…bmm2 task
adding samtools functionality
b2993fe
cleaned up samtools functionality
5a703b8
@tanyasarkjain
some small mem changes to make compatible with docker
21a99f8
adding deepvariant (though still potentially need to resolve singular…
346ecc3 
…ity issues)
@tanyasarkjain
added gatk4haplotype caller
48592c7
@tanyasarkjain
Update README.md
d874058
@tanyasarkjain
Add files via upload
e6415b4 
adding metro map
@tanyasarkjain
Update README.md
59fd18b 
adding image
@tanyasarkjain
Add files via upload
7e3e17a
@tanyasarkjain
Update README.md
86bd969
@tanyasarkjain
Add files via upload
0f99dd1
@tanyasarkjain
Update README.md
c360869
@tanyasarkjain
Update README.md
47e72e7 
Modified read me
@tanyasarkjain
Update README.md
62bc0cc
@tanyasarkjain
Update README.md
3912721
@tanyasarkjain
Update README.md
e52b756
@tanyasarkjain
Update README.md
0e72179
@tanyasarkjain
Add files via upload
9c9a89a
@tanyasarkjain
seperate workfall for bam variant calling
303543e
@tanyasarkjain
added regions to deepvariant
56ea0cd
deepvariant working on savio cluster (singularity)
24aee57
@tanyasarkjain
changes
b77019c
@tanyasarkjain
change
646bf0a
succ run + changing to process_high from process_large
cf172cf
@tanyasarkjain
trgt workflow
b8075d8
@tanyasarkjain
change to fasta
d2609e7
sateeshperi
sateeshperi requested changes Nov 29, 2024
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fix test profile

@fellen31
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Still some unanswered questions/comments.

@sateeshperi
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Things to do;

  • Update nf-core subworkflows
  • Update docs/usage.md & docs/output.md
  • Make a proper test_full samplesheet (currently uses the same as test profile)

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Reviewers

@sateeshperi sateeshperi sateeshperi requested changes

@fellen31 fellen31 Awaiting requested review from fellen31

Requested changes must be addressed to merge this pull request.

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3 participants
@tanyasarkjain @fellen31 @sateeshperi