Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add pairwise gene variation subworkflow / nf-tools v3.2.0 #5

Open
wants to merge 69 commits into
base: dev
Choose a base branch
from
Open

Add pairwise gene variation subworkflow / nf-tools v3.2.0 #5

wants to merge 69 commits into from

Conversation

OlivierCoen
Copy link
Collaborator

PR checklist

  • add step to compute pairwise gene variation (inspired by Genorm) and get most stable genes with respect to this measure
  • include update of nf-tools version 3.2.0

@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
rename edger and deseq2 output files and channel
e68d2f5
@OlivierCoen
fix nf-core linter erros
0ef10a9
@OlivierCoen
add labels to modules
ce3bc3e
@OlivierCoen
update tests nd various functionnalities to pass CI tests
a2068af
OlivierCoen and others added 25 commits January 16, 2025 11:54
@OlivierCoen
create subworkflow to compute pairwise fene variation
5b6c64e
@OlivierCoen
add pairwise gene variation subworkflow to main workflow
9a30679
@OlivierCoen
fix bugs with pairwise gene variation
3e98355
@OlivierCoen
fix bugs with computation of m measures
7ebbea3
@OlivierCoen
handle g:Profiler server breakdown in id mapping step
517169c
@OlivierCoen
add parameters for g:Profiler
4fa2148
@OlivierCoen
add section in multiqc
47596ef
@OlivierCoen
fix case when nb genes equals GENE_CHUNK_SIZE
e8cc91a
@OlivierCoen
fix difference of results between the pairwise gene variation workflo…
8337d52 
…w and the genorm python package
@OlivierCoen
fix difference of results between the pairwise gene variation workflo…
05975b7 
…w and the genorm python package
@OlivierCoen
fix difference of results between the pairwise gene variation workflo…
898ef35 
…w and the genorm python package
@OlivierCoen
redirect calls to g:Profiler beta API server when main one is down
a3a341e
@OlivierCoen
change expression status computation and configuration in multiqc
c1cc181
@OlivierCoen
change export of statistics fata and siplay in multiqc - fix gene ord…
ccb1550 
…er issue when displaying log count distribution for the most stable genes
@OlivierCoen
change export of statistics fata and siplay in multiqc - fix gene ord…
a48c2db 
…er issue when displaying log count distribution for the most stable genes
@OlivierCoen
Template update for nf-core/tools version 3.1.2
735537c
@OlivierCoen
Merge pull request nf-core#3 from OlivierCoen/TEMPLATE
837ecf5 
Template update for nf-core/tools version 3.1.2
@OlivierCoen
Merge branch 'TEMPLATE' into dev
d7ee8a6 
# Conflicts:
#	.github/workflows/awsfulltest.yml
#	.github/workflows/ci.yml
#	.gitignore
#	.nf-core.yml
#	CITATIONS.md
#	README.md
#	assets/email_template.html
#	assets/multiqc_config.yml
#	assets/schema_input.json
#	conf/base.config
#	conf/modules.config
#	conf/test.config
#	conf/test_full.config
#	docs/output.md
#	docs/usage.md
#	main.nf
#	modules.json
#	modules/nf-core/multiqc/environment.yml
#	modules/nf-core/multiqc/main.nf
#	modules/nf-core/multiqc/tests/main.nf.test.snap
#	nextflow.config
#	nextflow_schema.json
#	subworkflows/local/utils_nfcore_stableexpression_pipeline/main.nf
#	subworkflows/nf-core/utils_nextflow_pipeline/main.nf
#	subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
#	subworkflows/nf-core/utils_nfcore_pipeline/main.nf
#	subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
#	workflows/stableexpression.nf
@OlivierCoen
merged TEMPLATE into dev
365135a
@nf-core-bot
Template update for nf-core/tools version 3.2.0
f59ae1c
@OlivierCoen
fixed bugs following merge with TEMPLATE
8b030fe
@OlivierCoen
merged with TEMPLATE
0421420
@OlivierCoen
fix issues with linting
37777da
@OlivierCoen
add test data; modify path to test data
9f51a32
@OlivierCoen
add check that merged count dataset is not empty
146991d
@OlivierCoen OlivierCoen self-assigned this Jan 31, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees

@OlivierCoen OlivierCoen

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@OlivierCoen @nf-core-bot