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Stabilisation / Completeness of pipeline #1

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wants to merge 33 commits into from
Closed

Stabilisation / Completeness of pipeline #1

wants to merge 33 commits into from

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OlivierCoen
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  • better error handling in gene id mapping step
  • modify output of gene id mapping
  • add gene metadata to gene statistics in the gene variation step
  • stabilised expressionatlas_getaccessions and expression_atlas (ignore / retry step according to exit status code)
  • handle multiple issue cases in normalisation steps (DESeq2 / EdgeR)
  • rewrote the gene variation step in python, using polars for better efficiency / stability
  • set expression atlas step in a separate workflow
  • replace nf-validation by nf-schema
  • add multiqc to pipeline
  • improve gene vriation statistics computation and visualisation in multiqc

PR checklist

  • This comment contains a description of changes (with reason).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Documentation has been updated.

@OlivierCoen
update metro map ;Update pre-commit hooks
50988b6
@OlivierCoen
fix comment and rename variable
e3bd4c5
@OlivierCoen
modified map_ids_to_ensembl.py to get gene metadata
1ba7847
@OlivierCoen
added gene metadata and original gene ids to variation coefficient ou…
6ef626e 
…tput file
@OlivierCoen
remove genes with at least one zero count by default; added parameter…
4d034e1 
… to skip this behaviour
@OlivierCoen
improved output of get_eatlas_accessions
5f73254
@OlivierCoen
fixed bug with DESeq2 caused by count rows having many zeros
6b49e00
@OlivierCoen
ignore issue with ExpressionAtlas R package when summary is unavailab…
41a6bd0 
…le; removed debug statement from modules
@OlivierCoen
handle idmapping in case when count file is empty
38ed6df
@OlivierCoen
removed allow_zeros argument
c4be7a8
@OlivierCoen
added check that count datasets do not get empty because of filtering…
82d3e37 
… during normalisation
@OlivierCoen
remove when statement from module main.nf files
2b82024
@OlivierCoen
separate merging step from get_variation_coefficients.R; translated g…
4bef904 
…et_variation_coefficients.R to python
@OlivierCoen
implemented get_variation_coefficients.py in polars
7890f7e
@OlivierCoen
fixed issue with deseq2 when design contains one condition
63728d2
@OlivierCoen
added option for gene variation computation method
cab4310
@OlivierCoen
fixed issues with idmapping not finding entries
97fce7e
@OlivierCoen
fixed issue with Expression Atlas Get data releasing more than one co…
808cb55 
…unt file for one single accession
@OlivierCoen
place Expression Atlas steps in a separate subworkflow
00e39c8
@OlivierCoen
improve error handling in expressionatlas getdata
f87ba65
@OlivierCoen
handle extra bug cases for expressionatlas getdata
58780f0
@OlivierCoen
update pipeline to latest nf-core specs
8b4dc63
@OlivierCoen
add multiqc to pipeline
1e37a19
@OlivierCoen
remove log transformation during normalisation steps
14211e2
@OlivierCoen
improve statistic computation and multiqc visualisation
a1cc1f2
@OlivierCoen
update documentation
a54fddf
@OlivierCoen OlivierCoen self-assigned this Jan 7, 2025
@OlivierCoen OlivierCoen force-pushed the dev branch 2 times, most recently from 7ed2467 to 308ccfc Compare January 7, 2025 13:53
@OlivierCoen
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Closing this pull request as I have more modifications to perform before merging. I'd like to get a pipeline ready for realease before asking for a PR

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