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Pull request - trying to add BSSNPer #223

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Pull request - trying to add BSSNPer #223

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AliaMW
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@AliaMW AliaMW commented Nov 25, 2021

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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/methylseq 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).
  • 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).

@AliaMW
Picard AddorReplaceRG process added
477d40e 
Adding intermediate step - add readgroups to BAM files - before adding BisSNP
@AliaMW
BsSNPer and markDuplicates extra channel
326236d 
Added new process AFTER markDuplicates to call SNPs
Added extra channel in markDuplicates output for new process
@AliaMW
Adding more to the BSSNPer process
8ae6ea8
@AliaMW
Hardcoded hg19 in BS-SNPer --fa
c906322 
Change it eventually
@AliaMW
Modified pipeline with bssnper
60ada19
@AliaMW
Comma deleted
e284fc5
@AliaMW
newline deleted
70d10b8
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@AliaMW AliaMW changed the base branch from master to dev November 25, 2021 10:54
@ewels ewels added the dsl1 label Nov 8, 2022
@sateeshperi
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hi @AliaMW could i ask about the status of this PR?

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@AliaMW @sateeshperi @ewels