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Feature intron counting #11

Merged
merged 12 commits into from
Jan 9, 2024
Merged

Feature intron counting #11

merged 12 commits into from
Jan 9, 2024

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atrull314
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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/scnanoseq 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>).
  • 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).

atrull314 and others added 12 commits November 8, 2023 10:46
@atrull314
Removing prowlertrimmer and cleaning up parameters
322e4bc
@atrull314
Removing expected cell count from a pipeline wide parameter to a samp…
db5f73f 
…le-specific one
@atrull314
Fixes for adding back intron retention method 1. Namely making sure t…
39c2d48 
…hat the prepare_gtf_transcript_to_exon accepts the updated gtf channel format, and also enabling infer_genes/transcripts when this method is chosen for isoquant
@lianov
adding default for required param
dab72b7
@lianov
added ucsc local modules for bed file generation
5b49761
@lianov
added nf-core rseqc read_distribution module
8cba77e
@lianov
added first pass at rseqc read distribution
c015e67
@lianov
removed stringtie modules
d391c0c
@lianov
updates to schema
b1da796
@lianov
updates to multiqc config
6a60b65
@atrull314
Changing intron retention method to rely solely on isoquant and clean…
d0ffe36 
…ing up as a result
@atrull314
Removing depreceated parameter from test config
85af2c3
@atrull314 atrull314 merged commit 42a8665 into dev Jan 9, 2024
2 of 6 checks passed
@atrull314 atrull314 deleted the feature_intron_counting branch January 9, 2024 23:19
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2 participants
@atrull314 @lianov