Code quality feedback#1

Draft

hdbeukel wants to merge 251 commits intofeedback-hermanfrom main

+3,165,237-120

This pull request is big! We're only showing the most recent 250 commits

Commits on Apr 7, 2023

Commits on Apr 10, 2023

Commits on Apr 11, 2023

Commits on Apr 12, 2023

adding openpyxl
nicomaper
committed

Commits on Apr 14, 2023

Commits on Apr 18, 2023

Commits on Apr 21, 2023

Commits on May 8, 2023

Commits on May 16, 2023

Commits on May 23, 2023

Commits on Jun 21, 2023

Commits on Jun 23, 2023

Commits on Jul 5, 2023

Commits on Jul 20, 2023

perc of DEGs is TG
nicomaper
committed

Commits on Sep 13, 2023

Commits on Sep 18, 2023

Commits on Sep 21, 2023

remove P_val parameter config file
nicomaper
committed
remove comment miniac_gw script getStats process
nicomaper
committed
Remove code duplication in main workflow
Herman DE BEUKELAER
committed
Add missing curly brace
Herman De Beukelaer
committed
Use switch for setting species id
Herman De Beukelaer
committed
Add missing breaks to switch
Herman De Beukelaer
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Exclude nextflow cache dir and logs from version control
Herman De Beukelaer
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Rename gene metadata files to match other file path structure
Herman De Beukelaer
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Rename MotMapsFile_gw and *_lb parameters to just MotifMapsFile
Herman De Beukelaer
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Refine gitignore
Herman De Beukelaer
committed
Correct GO enrichment output file name
nicomaper
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Fix bug for checking motif mappings exist
nicomaper
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Merge pull request #6 from VIB-PSB/hotfix/motmap-check-if-exists
nicomaper
authored
Merge branch 'main' into dev
nicomaper
committed
Merge branch 'dev' into feature/remove-duplication-from-main-workflow
Herman De Beukelaer
committed
Merge branch 'dev' into feature/remove-commented-code
nicomaper
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Ignore bin folder
Herman De Beukelaer
committed

Commits on Sep 25, 2023

Add gitignore
Herman De Beukelaer
committed
Prepare workflows for e2e testing
Herman De Beukelaer
committed
Ignore test outputs
Herman De Beukelaer
committed
Add first workflow e2e test
Herman De Beukelaer
committed
Pass shuffle count as variable to process stats correctly
Herman De Beukelaer
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Provide shuffle seed for reproducible test results
Herman De Beukelaer
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Add maize test input filtered for chromosome 1
Herman De Beukelaer
committed
Update test scenario for maize genome-wide
Herman De Beukelaer
committed
Ignore SLURM output and error files
Herman De Beukelaer
committed
Fix test file paths
Herman De Beukelaer
committed
Fix test input folder names
Herman De Beukelaer
committed
Reduce maize non-conding genome to chr1 for testing
Herman De Beukelaer
committed
Reduce promotor maize promotor coordinates files to chr1 for testing
Herman De Beukelaer
committed
Download test motif mapping files only if not already present
Herman De Beukelaer
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Rename variables to clarify it's maize
Herman De Beukelaer
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Install nf-test only once
Herman De Beukelaer
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Fix maize test folder names
Herman De Beukelaer
committed

Commits on Sep 26, 2023

Output CSV instead of Excel in test runs
Herman De Beukelaer
committed
Fix csv flag not passed from main workflow
Herman De Beukelaer
committed
Fix -csv bool flag in python scripts
Herman De Beukelaer
committed
Remove metavar from csv flag
Herman De Beukelaer
committed
Get rid of non-working boolean flag
Herman De Beukelaer
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Revert "Get rid of non-working boolean flag"
Herman De Beukelaer
committed
Use .csv extension for writing csv files
Herman De Beukelaer
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Revert "Revert "Get rid of non-working boolean flag""
Herman De Beukelaer
committed
Automatically infer export type from file extension
Herman De Beukelaer
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Add arabidopsis test data
Herman De Beukelaer
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Check csv/excel in special case with empty output too
Herman De Beukelaer
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Fix integrative results output paths
Herman De Beukelaer
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Add maize_v4 gw test snapshot
Herman De Beukelaer
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Add maize_v4 locus-based test case
Herman De Beukelaer
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Sort TF families in motif centric output for reproducible results
Herman De Beukelaer
committed
Update test snapshot: maize_v4 genome_wide
Herman De Beukelaer
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Add maize_v4 locus-based test case
Herman De Beukelaer
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Sort output of bps stats
Herman De Beukelaer
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Update test snapshot for maize test cases (final)
Herman De Beukelaer
committed

Commits on Sep 27, 2023

Add arabidopsis test cases
Herman De Beukelaer
committed
Fix second gene annotation
Herman De Beukelaer
committed
Merge branch 'hotfix/second-gene-annot' into feature/automated-e2e-test
Herman De Beukelaer
committed
Add test snapshot
Herman De Beukelaer
committed
Merge pull request #8 from VIB-PSB/hotfix/second-gene-annot
nicomaper
authored
Merge branch 'main' into dev
nicomaper
committed
Merge branch 'dev' into feature/remove-commented-code
nicomaper
committed
Merge branch 'dev' into feature/remove-duplication-from-main-workflow
nicomaper
committed
Merge branch 'dev' into feature/automated-e2e-test
nicomaper
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Update test snapshots
Herman De Beukelaer
committed
Merge branch 'feature/automated-e2e-test' of github.com:VIB-PSB/MINI-AC into feature/automated-e2e-test
Herman De Beukelaer
committed
Setup github test workflow
Herman De Beukelaer
committed
Specify singularity version
Herman De Beukelaer
committed
Fix test config preparation
Herman De Beukelaer
committed
Try to resolve tmp folder for singularity
Herman De Beukelaer
committed
Download arabidopsis test motif mapping files from floppy instead of zenodo (faster)
Herman De Beukelaer
committed
Attempt to use GitHub runner temp dir
Herman De Beukelaer
committed
Rename job
Herman De Beukelaer
committed
Atempt again to set tmp dir
Herman De Beukelaer
committed
Explicitly specify bash shell for nf-test
Herman De Beukelaer
committed
Try to symlink bash
Herman De Beukelaer
committed
Try running on mac OS
Herman De Beukelaer
committed
Explicitly setup java
Herman De Beukelaer
committed
Try again to setup java
Herman De Beukelaer
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Enable SSH debugging
Herman De Beukelaer
committed
Debug after failed nf-test run
Herman De Beukelaer
committed
Try to fix tmp dir
Herman De Beukelaer
committed
Try to fix tmp dir
Herman De Beukelaer
committed
Try to fix tmp dir
Herman De Beukelaer
committed
Fix default seed (none)
Herman De Beukelaer
committed

Commits on Sep 28, 2023

Merge branch 'feature/automated-e2e-test' into feature/remove-duplication-from-main-workflow
Herman De Beukelaer
committed
Revert accidental change of p-value for locus-based
Herman De Beukelaer
committed
Provide gene coords for gw mode only
Herman De Beukelaer
committed
Correct test input file paths due to rename
Herman De Beukelaer
committed
Update of documentation for maize genome version NAM5.0 support, and zma_v4 and zma_v5 folders/files changes
nicomaper
committed
correction of minor typo
nicomaper
committed
Pass full params object from main workflow to gw and lb workflows
Herman De Beukelaer
committed
Make the usage command more general, specify what species/mode the example should be, and separating the wget commands based on species/genome version
nicomaper
committed
Merge pull request #10 from VIB-PSB/hotfix/documentation-update
nicomaper
authored
correct typo of wget download command missing -O flag
nicomaper
committed

Commits on Oct 5, 2023

Add newline at end of gitignore
Herman DE BEUKELAER
committed
Remove script to run tests on SLURM and refactor GitHub action
Herman DE BEUKELAER
committed
Fix path when fetching zma_v4 chr1 motif mapping test files
Herman DE BEUKELAER
committed
update citation
nicomaper
committed
update citation
nicomaper
committed
Merge pull request #14 from VIB-PSB/hotfix/update-tpj-citation
nicomaper
authored
Merge branch 'main' into dev
Herman DE BEUKELAER
committed
Merge branch 'dev' into feature/automated-e2e-test
Herman DE BEUKELAER
committed
Attempt to remove empty workflow block from tests
Herman DE BEUKELAER
committed
Merge pull request #9 from VIB-PSB/feature/automated-e2e-test
nicomaper
authored

Commits on Oct 6, 2023

Merge pull request #15 from VIB-PSB/dev
nicomaper
authored

Commits on Oct 16, 2023

Merge branch 'dev' into feature/remove-duplication-from-main-workflow
Herman DE BEUKELAER
committed

Commits on Oct 27, 2023

Merge pull request #3 from VIB-PSB/feature/remove-duplication-from-main-workflow
nicomaper
authored

Commits on May 13, 2024

Merge branch 'dev'
Nicolas MANOSALVA PEREZ
committed
Merge branch 'dev' into feature/remove-commented-code
hdbeukel
authored
Merge pull request #2 from VIB-PSB/feature/remove-commented-code
hdbeukel
authored
Merge pull request #20 from VIB-PSB/main
nicomaper
authored
Merge pull request #19 from VIB-PSB/dev
hdbeukel
authored
Merge branch 'main' of https://github.com/VIB-PSB/MINI-AC
Nicolas MANOSALVA PEREZ
committed
Merge pull request #21 from VIB-PSB/dev
nicomaper
authored
update gitignore on slurm output files
Nicolas MANOSALVA PEREZ
committed
input ACR directory is given as a channel to the gw and lb workflows
Nicolas MANOSALVA PEREZ
committed

Commits on May 14, 2024

scripts for run of MINI-AC using iCREs - first commit
Nicolas MANOSALVA PEREZ
committed
Gene sets to run the example test
Nicolas MANOSALVA PEREZ
committed
updated gitignore to not upload icres bed fies (too big) and icres output files (confidential)
Nicolas MANOSALVA PEREZ
committed
MINI-AC iCREs config file
Nicolas MANOSALVA PEREZ
committed
Making the commented annotations more homogeneous
Nicolas MANOSALVA PEREZ
committed
Documentation update for iCREs-based MINI-AC
Nicolas MANOSALVA PEREZ
committed
Ignoring the files within "outputs_icres" but not the folder itself
Nicolas MANOSALVA PEREZ
committed
Keep empty folders with icres and icres outputs
Nicolas MANOSALVA PEREZ
committed

Commits on May 15, 2024

iCREs documentation update
Nicolas MANOSALVA PEREZ
committed

Commits on May 23, 2024

Documentation update
Nicolas MANOSALVA PEREZ
committed
Correction of code annotation
Nicolas MANOSALVA PEREZ
committed
Update on arguments parsing options
Nicolas MANOSALVA PEREZ
committed
Code annotation type
Nicolas MANOSALVA PEREZ
committed
Removal of nargs parameter in arguments parsing
Nicolas MANOSALVA PEREZ
committed
Merge pull request #22 from VIB-PSB/feature/icres-based-grns
nicomaper
authored

Commits on May 24, 2024

Merge pull request #23 from VIB-PSB/dev
nicomaper
authored

Commits on Jul 31, 2024

Making the iCREs files public with download instructions
Nicolas MANOSALVA PEREZ
committed
Merge pull request #24 from VIB-PSB/feature/icres-based-grns
nicomaper
authored