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First release! #4

Merged
merged 79 commits into from
Aug 2, 2024
Merged

First release! #4

merged 79 commits into from
Aug 2, 2024

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avani-bhojwani
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PR checklist

  • [N/A] 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/denovotranscript 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.
  • [N/A] CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

avani-bhojwani and others added 30 commits June 27, 2024 14:46
@avani-bhojwani
add test data
d94742c
@avani-bhojwani
update samplesheet
4f9ff2d
@avani-bhojwani
add fastq_trim_fastp_fastqc
b6c30df
@avani-bhojwani
added sortmerna
0266138
@avani-bhojwani
updated fastqc order
3599e4a
@avani-bhojwani
addded config for pre-processing
c79b8a8
@avani-bhojwani
patch sortmerna module
94f57fb
@avani-bhojwani
add cat_fastq step
78056ff
@avani-bhojwani
added trinity steps
8bf57d7
@avani-bhojwani
added rnaspades
31abbef
@avani-bhojwani
added soft and hard filtered transcripts
a05bdba
@avani-bhojwani
fix channel names
f8cc683
@avani-bhojwani
cat assembled transcripts
4c1433d
@avani-bhojwani
added cat_cat module
4791813
@avani-bhojwani
add evigene tr2aacds
b03fb52
@avani-bhojwani
added busco module
fbed1bf
@avani-bhojwani
added salmon steps
9cb0264
@avani-bhojwani
add busco_lineage
9bd7fed
@avani-bhojwani
rearrage imports
a3a2283
@avani-bhojwani
remove completed comments
d4e4fde
@avani-bhojwani
patch modules
282a8f2
@avani-bhojwani
update params and descriptions
c4b360b
@avani-bhojwani
add documentation
3a105ec
@avani-bhojwani
minor comments and params updates
365b5fd
@avani-bhojwani
add rnaquast
6733b90
@avani-bhojwani
add tx2gene step
fb5b919
@avani-bhojwani
update label and file naming
03d716d
@avani-bhojwani
bump version and remove gene_mark
c539fb0
@avani-bhojwani
add transrate
950a6ff
@avani-bhojwani
Update denovotranscript_metro_map.drawio.svg
081ebc4
mashehu
mashehu reviewed Jul 19, 2024
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avani-bhojwani and others added 2 commits July 19, 2024 14:42
@avani-bhojwani @mashehu
Update docs/output.md
198f448 
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@avani-bhojwani @mashehu
Update CHANGELOG.md
28f0502 
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@avani-bhojwani
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Thank you for reviewing! I am finished with all the changes

@avani-bhojwani
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@mashehu @fbdtemme Sorry, just waiting for your approval to go ahead with merging

mashehu
mashehu approved these changes Jul 23, 2024
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@mashehu mashehu left a comment

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some smaller things left. rest looks good! nice job!

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fbdtemme
fbdtemme approved these changes Jul 23, 2024
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Looks good to me as well! Just one more small suggestion.

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avani-bhojwani and others added 13 commits July 24, 2024 20:42
@avani-bhojwani avani-bhojwani merged commit 503dff7 into master Aug 2, 2024
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@fbdtemme fbdtemme fbdtemme approved these changes

@mashehu mashehu mashehu approved these changes

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3 participants
@avani-bhojwani @mashehu @fbdtemme