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Code quality feedback #1

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Commits on Apr 7, 2023

  1. Dockerfile

    sathi committed Apr 7, 2023
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  2. Update docker-publish.yml

    @sanderthierens
    sanderthierens authored Apr 7, 2023
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  3. Update docker-publish.yml

    @sanderthierens
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  4. Update docker-publish.yml

    @sanderthierens
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  5. Update docker-publish.yml

    @sanderthierens
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  6. Update docker-publish.yml

    @sanderthierens
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  7. temp back to old yml

    @sanderthierens
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  8. dockerfile and requirements changed for miniac

    @nicomaper
    nicomaper committed Apr 7, 2023
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  9. Merge branch 'main' of https://github.com/VIB-PSB/MINI-AC into main

    @nicomaper
    nicomaper committed Apr 7, 2023
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  10. correct bedtools version 2.27

    @nicomaper
    nicomaper committed Apr 7, 2023
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  11. correct bedtools version 2.27.0

    @nicomaper
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  12. dcoker image bedtools 2.27.1+dfsg-4ubuntu1

    @nicomaper
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  13. space after

    @nicomaper
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  14. bedtools version 2.27.0+dfsg-5

    @nicomaper
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Commits on Apr 10, 2023

  1. no bedtools, test for the rest

    @nicomaper
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  2. install bedtools with wget

    @nicomaper
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  3. using biocontainers

    @nicomaper
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Commits on Apr 11, 2023

  1. bedops and samtools test via biocontainers

    @nicomaper
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  2. bedtools, bedops and samtools via bios and pip3 after python3 inst

    @nicomaper
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  3. using only FROM biocontainer and installing there python3

    @nicomaper
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  4. FROM biocontainer first line

    @nicomaper
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  5. multistage build

    @nicomaper
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  6. inverted builds; first biocontainer and then python3

    @nicomaper
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  7. only one FROM: biocontainers. Trying apt-get

    @nicomaper
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  8. only one FROM: biocontainers. No apt-get update

    @nicomaper
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  9. user root

    @nicomaper
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  10. user root apt-get update

    @nicomaper
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  11. test wget bedtools

    @nicomaper
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  12. test wget make bedtools

    @nicomaper
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  13. test wget make gcc bedtools

    @nicomaper
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  14. test wget make gcc zlib1g-dev bedtools

    @nicomaper
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  15. test wget make g++ build-essential

    @nicomaper
    nicomaper committed Apr 11, 2023
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  16. install conda

    @nicomaper
    nicomaper committed Apr 11, 2023
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  17. install conda

    @nicomaper
    nicomaper committed Apr 11, 2023
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  18. install conda

    @nicomaper
    nicomaper committed Apr 11, 2023
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  19. install conda

    @nicomaper
    nicomaper committed Apr 11, 2023
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  20. new docker image

    sathi committed Apr 11, 2023
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Commits on Apr 12, 2023

  1. adding openpyxl

    @nicomaper
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Commits on Apr 14, 2023

  1. no requirements

    @nicomaper
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  2. Removed file from repository but kept locally

    @nicomaper
    nicomaper committed Apr 14, 2023
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  3. first code commit

    @nicomaper
    nicomaper committed Apr 14, 2023
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Commits on Apr 17, 2023

  1. updated .gitignore

    @nicomaper
    nicomaper committed Apr 17, 2023
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  2. removing files that shoulve been ignored

    @nicomaper
    nicomaper committed Apr 17, 2023
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  3. tutorial and config file

    @nicomaper
    nicomaper committed Apr 17, 2023
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  4. Update README.md

    @nicomaper
    nicomaper authored Apr 17, 2023
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  5. Update README.md

    @nicomaper
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  6. Update README.md

    @nicomaper
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  7. Update README.md

    @nicomaper
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Commits on Apr 18, 2023

  1. Fixing nextflow script not finding NO_FILE

    @nicomaper
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  2. Merge branch 'main' of https://github.com/VIB-PSB/MINI-AC into main

    @nicomaper
    nicomaper committed Apr 18, 2023
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Commits on Apr 21, 2023

  1. Update README.md

    @nicomaper
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  2. Update README.md

    @nicomaper
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  3. Update configuration_pipeline.md

    @nicomaper
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Commits on Apr 28, 2023

  1. READMEs for motif mapping versions added

    @nicomaper
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  2. Merge branch 'main' of https://github.com/VIB-PSB/MINI-AC into main

    @nicomaper
    nicomaper committed Apr 28, 2023
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  3. Update README.md

    @nicomaper
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  4. check if motif mapping files downloaded correctly

    @nicomaper
    nicomaper committed Apr 28, 2023
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  5. Update README.md

    @nicomaper
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  6. Update configuration_pipeline.md

    @nicomaper
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Commits on May 8, 2023

  1. CREATING LICENSE

    @nicomaper
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  2. Update README.md

    @nicomaper
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Commits on May 16, 2023

  1. Update README.md

    @nicomaper
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  2. Update README_MINI_ath_2021.1_motif_mappings.txt

    @nicomaper
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  3. Update configuration_pipeline.md

    @nicomaper
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  4. Update README.md

    @nicomaper
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  5. Update README.md

    @nicomaper
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  6. Update configuration_pipeline.md

    @nicomaper
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  7. Update README.md

    @nicomaper
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  8. Update README.md

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  9. Update README.md

    @nicomaper
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  10. Update README.md

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  11. Update README.md

    @nicomaper
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  12. motif ID fix of integrative network visualization node attributes

    @nicomaper
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  13. Update README.md

    @nicomaper
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  14. Update configuration_pipeline.md

    @nicomaper
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  15. update config file without absolute paths

    @nicomaper
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  16. Update README.md

    @nicomaper
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  17. Update README.md

    @nicomaper
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  18. Update configuration_pipeline.md

    @nicomaper
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Commits on May 17, 2023

  1. Update configuration_pipeline.md

    @nicomaper
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  2. Update configuration_pipeline.md

    @nicomaper
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  3. Update configuration_pipeline.md

    @nicomaper
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  4. Update configuration_pipeline.md

    @nicomaper
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  5. Update README.md

    @nicomaper
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  6. check acr channel is not empty

    @nicomaper
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Commits on May 23, 2023

  1. Update README.md

    @nicomaper
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  2. Update README.md

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Commits on May 26, 2023

  1. Update README.md

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  2. Update configuration_pipeline.md

    @nicomaper
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  3. Update configuration_pipeline.md

    @nicomaper
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  4. Update configuration_pipeline.md

    @nicomaper
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  5. Update README.md

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Commits on Jun 21, 2023

  1. maize V5 data files

    @nicomaper
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  2. update of main script with elif statements

    @nicomaper
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Commits on Jun 23, 2023

  1. updated obo and TF-fam file of maize_v5

    @nicomaper
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  2. remove not ignored file

    @nicomaper
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Commits on Jul 5, 2023

  1. update maize v5 gene metadata table

    @nicomaper
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  2. updated .gitignore

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  3. maize v5

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Commits on Jul 20, 2023

  1. perc of DEGs is TG

    @nicomaper
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Commits on Sep 12, 2023

  1. Update configuration_pipeline.md

    @nicomaper
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  2. Update configuration_pipeline.md

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  3. Create FAQ.md

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  4. Update README.md

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  5. Update README.md

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  6. Update README.md

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  7. motif mappings READMEs update

    @nicomaper
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Commits on Sep 13, 2023

  1. change folders names to zma_v4, update main script accordingly, and u… 

    …pdate config file for slurm
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  2. comment change SGE to SLURM

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  3. Update README.md

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Commits on Sep 18, 2023

  1. Update README.md

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  2. Update LICENSE

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Commits on Sep 21, 2023

  1. remove P_val parameter config file

    @nicomaper
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  2. remove comment miniac_gw script getStats process

    @nicomaper
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  3. Remove code duplication in main workflow

    Herman DE BEUKELAER committed Sep 21, 2023
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  4. Add missing curly brace

    Herman De Beukelaer committed Sep 21, 2023
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  5. Use switch for setting species id

    Herman De Beukelaer committed Sep 21, 2023
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  6. Add missing breaks to switch

    Herman De Beukelaer committed Sep 21, 2023
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  7. Exclude nextflow cache dir and logs from version control

    Herman De Beukelaer committed Sep 21, 2023
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  8. Rename gene metadata files to match other file path structure

    Herman De Beukelaer committed Sep 21, 2023
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  9. Rename MotMapsFile_gw and *_lb parameters to just MotifMapsFile

    Herman De Beukelaer committed Sep 21, 2023
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  10. Refine gitignore

    Herman De Beukelaer committed Sep 21, 2023
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  11. Correct GO enrichment output file name

    @nicomaper
    nicomaper committed Sep 21, 2023
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  12. Fix bug for checking motif mappings exist

    @nicomaper
    nicomaper committed Sep 21, 2023
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  13. Merge pull request #6 from VIB-PSB/hotfix/motmap-check-if-exists 

    Fix bug for checking motif mappings exist
    @nicomaper
    nicomaper authored Sep 21, 2023
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  14. Merge branch 'main' into dev

    @nicomaper
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  15. Merge branch 'dev' into feature/remove-duplication-from-main-workflow

    Herman De Beukelaer committed Sep 21, 2023
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  16. Merge branch 'dev' into feature/remove-commented-code

    @nicomaper
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  17. Ignore bin folder

    Herman De Beukelaer committed Sep 21, 2023
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Commits on Sep 25, 2023

  1. Add gitignore

    Herman De Beukelaer committed Sep 25, 2023
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  2. Prepare workflows for e2e testing

    Herman De Beukelaer committed Sep 25, 2023
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  3. Ignore test outputs

    Herman De Beukelaer committed Sep 25, 2023
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  4. Add first workflow e2e test

    Herman De Beukelaer committed Sep 25, 2023
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  5. Pass shuffle count as variable to process stats correctly

    Herman De Beukelaer committed Sep 25, 2023
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  6. Provide shuffle seed for reproducible test results

    Herman De Beukelaer committed Sep 25, 2023
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  7. Add maize test input filtered for chromosome 1

    Herman De Beukelaer committed Sep 25, 2023
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  8. Update test scenario for maize genome-wide

    Herman De Beukelaer committed Sep 25, 2023
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  9. Ignore SLURM output and error files

    Herman De Beukelaer committed Sep 25, 2023
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  10. Fix test file paths

    Herman De Beukelaer committed Sep 25, 2023
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  11. Fix test input folder names

    Herman De Beukelaer committed Sep 25, 2023
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  12. Reduce maize non-conding genome to chr1 for testing

    Herman De Beukelaer committed Sep 25, 2023
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  13. Reduce promotor maize promotor coordinates files to chr1 for testing

    Herman De Beukelaer committed Sep 25, 2023
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  14. Download test motif mapping files only if not already present

    Herman De Beukelaer committed Sep 25, 2023
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  15. Rename variables to clarify it's maize

    Herman De Beukelaer committed Sep 25, 2023
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  16. Install nf-test only once

    Herman De Beukelaer committed Sep 25, 2023
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  17. Fix maize test folder names

    Herman De Beukelaer committed Sep 25, 2023
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Commits on Sep 26, 2023

  1. Output CSV instead of Excel in test runs

    Herman De Beukelaer committed Sep 26, 2023
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  2. Fix csv flag not passed from main workflow

    Herman De Beukelaer committed Sep 26, 2023
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  3. Fix -csv bool flag in python scripts

    Herman De Beukelaer committed Sep 26, 2023
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  4. Remove metavar from csv flag

    Herman De Beukelaer committed Sep 26, 2023
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  5. Get rid of non-working boolean flag

    Herman De Beukelaer committed Sep 26, 2023
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  6. Revert "Get rid of non-working boolean flag" 

    This reverts commit 14a4f6f.
    Herman De Beukelaer committed Sep 26, 2023
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  7. Use .csv extension for writing csv files

    Herman De Beukelaer committed Sep 26, 2023
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  8. Revert "Revert "Get rid of non-working boolean flag"" 

    This reverts commit 42e3bea.
    Herman De Beukelaer committed Sep 26, 2023
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  9. Automatically infer export type from file extension

    Herman De Beukelaer committed Sep 26, 2023
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  10. Add arabidopsis test data

    Herman De Beukelaer committed Sep 26, 2023
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  11. Check csv/excel in special case with empty output too

    Herman De Beukelaer committed Sep 26, 2023
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  12. Fix integrative results output paths

    Herman De Beukelaer committed Sep 26, 2023
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  13. Add maize_v4 gw test snapshot

    Herman De Beukelaer committed Sep 26, 2023
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  14. Add maize_v4 locus-based test case

    Herman De Beukelaer committed Sep 26, 2023
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  15. Sort TF families in motif centric output for reproducible results

    Herman De Beukelaer committed Sep 26, 2023
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  16. Update test snapshot: maize_v4 genome_wide

    Herman De Beukelaer committed Sep 26, 2023
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  17. Add maize_v4 locus-based test case

    Herman De Beukelaer committed Sep 26, 2023
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  18. Sort output of bps stats

    Herman De Beukelaer committed Sep 26, 2023
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  19. Update test snapshot for maize test cases (final)

    Herman De Beukelaer committed Sep 26, 2023
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Commits on Sep 27, 2023

  1. Add arabidopsis test cases

    Herman De Beukelaer committed Sep 27, 2023
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  2. Fix second gene annotation

    Herman De Beukelaer committed Sep 27, 2023
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  3. Merge branch 'hotfix/second-gene-annot' into feature/automated-e2e-test

    Herman De Beukelaer committed Sep 27, 2023
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  4. Add test snapshot

    Herman De Beukelaer committed Sep 27, 2023
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  5. Merge pull request #8 from VIB-PSB/hotfix/second-gene-annot 

    Fix second gene annotation - cheked in output network files the median number of TGs per TF, and it increased ~25%, which means that adding the argument "--second_gene_dist 500" had an impact on the final networks.
    @nicomaper
    nicomaper authored Sep 27, 2023
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  6. Merge branch 'main' into dev

    @nicomaper
    nicomaper committed Sep 27, 2023
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  7. Merge branch 'dev' into feature/remove-commented-code

    @nicomaper
    nicomaper committed Sep 27, 2023
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  8. Merge branch 'dev' into feature/remove-duplication-from-main-workflow

    @nicomaper
    nicomaper committed Sep 27, 2023
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  9. Merge branch 'dev' into feature/automated-e2e-test

    @nicomaper
    nicomaper committed Sep 27, 2023
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  10. Update test snapshots

    Herman De Beukelaer committed Sep 27, 2023
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  11. Merge branch 'feature/automated-e2e-test' of github.com:VIB-PSB/MINI-… 

    …AC into feature/automated-e2e-test
    Herman De Beukelaer committed Sep 27, 2023
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  12. Setup github test workflow

    Herman De Beukelaer committed Sep 27, 2023
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  13. Specify singularity version

    Herman De Beukelaer committed Sep 27, 2023
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  14. Fix test config preparation

    Herman De Beukelaer committed Sep 27, 2023
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  15. Try to resolve tmp folder for singularity

    Herman De Beukelaer committed Sep 27, 2023
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  16. Download arabidopsis test motif mapping files from floppy instead of … 

    …zenodo (faster)
    Herman De Beukelaer committed Sep 27, 2023
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  17. Attempt to use GitHub runner temp dir

    Herman De Beukelaer committed Sep 27, 2023
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  18. Rename job

    Herman De Beukelaer committed Sep 27, 2023
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  19. Atempt again to set tmp dir

    Herman De Beukelaer committed Sep 27, 2023
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  20. Explicitly specify bash shell for nf-test

    Herman De Beukelaer committed Sep 27, 2023
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  21. Try to symlink bash

    Herman De Beukelaer committed Sep 27, 2023
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  22. Try running on mac OS

    Herman De Beukelaer committed Sep 27, 2023
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  23. Explicitly setup java

    Herman De Beukelaer committed Sep 27, 2023
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  24. Try again to setup java

    Herman De Beukelaer committed Sep 27, 2023
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  25. Enable SSH debugging

    Herman De Beukelaer committed Sep 27, 2023
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  26. Debug after failed nf-test run

    Herman De Beukelaer committed Sep 27, 2023
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  27. Try to fix tmp dir

    Herman De Beukelaer committed Sep 27, 2023
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  28. Try to fix tmp dir

    Herman De Beukelaer committed Sep 27, 2023
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  29. Try to fix tmp dir

    Herman De Beukelaer committed Sep 27, 2023
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  30. Fix default seed (none)

    Herman De Beukelaer committed Sep 27, 2023
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Commits on Sep 28, 2023

  1. Merge branch 'feature/automated-e2e-test' into feature/remove-duplica… 

    …tion-from-main-workflow
    Herman De Beukelaer committed Sep 28, 2023
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  2. Revert accidental change of p-value for locus-based

    Herman De Beukelaer committed Sep 28, 2023
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  3. Provide gene coords for gw mode only

    Herman De Beukelaer committed Sep 28, 2023
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  4. Correct test input file paths due to rename

    Herman De Beukelaer committed Sep 28, 2023
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  5. Update of documentation for maize genome version NAM5.0 support, and … 

    …zma_v4 and zma_v5 folders/files changes
    @nicomaper
    nicomaper committed Sep 28, 2023
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  6. correction of minor typo

    @nicomaper
    nicomaper committed Sep 28, 2023
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  7. Pass full params object from main workflow to gw and lb workflows

    Herman De Beukelaer committed Sep 28, 2023
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  8. Make the usage command more general, specify what species/mode the ex… 

    …ample should be, and separating the wget commands based on species/genome version
    @nicomaper
    nicomaper committed Sep 28, 2023
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  9. Merge pull request #10 from VIB-PSB/hotfix/documentation-update 

    Updating documentation to maize genome version 5 addition
    @nicomaper
    nicomaper authored Sep 28, 2023
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  10. correct typo of wget download command missing -O flag

    @nicomaper
    nicomaper committed Sep 28, 2023
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Commits on Sep 29, 2023

  1. Merge pull request #12 from VIB-PSB/hotfix/documentation-update 

    Correct typo of wget download command missing -O flag
    @hdbeukel
    hdbeukel authored Sep 29, 2023
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  2. Merge branch 'main' into dev

    @nicomaper
    nicomaper committed Sep 29, 2023
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  3. Merge branch 'dev' into feature/remove-duplication-from-main-workflow

    @nicomaper
    nicomaper committed Sep 29, 2023
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  4. update on .gitignore

    @nicomaper
    nicomaper committed Sep 29, 2023
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  5. update on .gitignore

    @nicomaper
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Commits on Oct 5, 2023

  1. Add newline at end of gitignore

    Herman DE BEUKELAER committed Oct 5, 2023
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  2. Remove script to run tests on SLURM and refactor GitHub action

    Herman DE BEUKELAER committed Oct 5, 2023
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  3. Fix path when fetching zma_v4 chr1 motif mapping test files

    Herman DE BEUKELAER committed Oct 5, 2023
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  4. update citation

    @nicomaper
    nicomaper committed Oct 5, 2023
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  5. update citation

    @nicomaper
    nicomaper committed Oct 5, 2023
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  6. Merge pull request #14 from VIB-PSB/hotfix/update-tpj-citation 

    Update of TPJ citation without volume, issue and page range.
    @nicomaper
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  7. Merge branch 'main' into dev

    Herman DE BEUKELAER committed Oct 5, 2023
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  8. Merge branch 'dev' into feature/automated-e2e-test

    Herman DE BEUKELAER committed Oct 5, 2023
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  9. Attempt to remove empty workflow block from tests

    Herman DE BEUKELAER committed Oct 5, 2023
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  10. Merge pull request #9 from VIB-PSB/feature/automated-e2e-test 

    Automated e2e test
    @nicomaper
    nicomaper authored Oct 5, 2023
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Commits on Oct 6, 2023

  1. Merge pull request #15 from VIB-PSB/dev 

    Release 1.1 - e2e test
    @nicomaper
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Commits on Oct 16, 2023

  1. Merge branch 'dev' into feature/remove-duplication-from-main-workflow

    Herman DE BEUKELAER committed Oct 16, 2023
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Commits on Oct 27, 2023

  1. Merge pull request #3 from VIB-PSB/feature/remove-duplication-from-ma… 

    …in-workflow

Remove code duplication in main workflow
    @nicomaper
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Commits on May 13, 2024

  1. Merge branch 'dev'

    Nicolas MANOSALVA PEREZ committed May 13, 2024
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  2. Merge branch 'dev' into feature/remove-commented-code

    @hdbeukel
    hdbeukel authored May 13, 2024
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  3. Merge pull request #2 from VIB-PSB/feature/remove-commented-code 

    Remove commented code
    @hdbeukel
    hdbeukel authored May 13, 2024
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  4. Merge pull request #20 from VIB-PSB/main 

    Main -> dev
    @nicomaper
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  5. Merge pull request #19 from VIB-PSB/dev 

    Dev
    @hdbeukel
    hdbeukel authored May 13, 2024
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  6. Merge branch 'main' of https://github.com/VIB-PSB/MINI-AC

    Nicolas MANOSALVA PEREZ committed May 13, 2024
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  7. Merge pull request #21 from VIB-PSB/dev 

    Dev
    @nicomaper
    nicomaper authored May 13, 2024
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  8. update gitignore on slurm output files

    Nicolas MANOSALVA PEREZ committed May 13, 2024
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  9. input ACR directory is given as a channel to the gw and lb workflows

    Nicolas MANOSALVA PEREZ committed May 13, 2024
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Commits on May 14, 2024

  1. scripts for run of MINI-AC using iCREs - first commit

    Nicolas MANOSALVA PEREZ committed May 14, 2024
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  2. Gene sets to run the example test

    Nicolas MANOSALVA PEREZ committed May 14, 2024
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  3. updated gitignore to not upload icres bed fies (too big) and icres ou… 

    …tput files (confidential)
    Nicolas MANOSALVA PEREZ committed May 14, 2024
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  4. MINI-AC iCREs config file

    Nicolas MANOSALVA PEREZ committed May 14, 2024
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  5. Making the commented annotations more homogeneous

    Nicolas MANOSALVA PEREZ committed May 14, 2024
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  6. Documentation update for iCREs-based MINI-AC

    Nicolas MANOSALVA PEREZ committed May 14, 2024
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  7. Ignoring the files within "outputs_icres" but not the folder itself

    Nicolas MANOSALVA PEREZ committed May 14, 2024
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  8. Keep empty folders with icres and icres outputs

    Nicolas MANOSALVA PEREZ committed May 14, 2024
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Commits on May 15, 2024

  1. iCREs documentation update

    Nicolas MANOSALVA PEREZ committed May 15, 2024
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Commits on May 23, 2024

  1. Documentation update

    Nicolas MANOSALVA PEREZ committed May 23, 2024
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  2. Correction of code annotation

    Nicolas MANOSALVA PEREZ committed May 23, 2024
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  3. Update on arguments parsing options

    Nicolas MANOSALVA PEREZ committed May 23, 2024
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  4. Code annotation type

    Nicolas MANOSALVA PEREZ committed May 23, 2024
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  5. Removal of nargs parameter in arguments parsing

    Nicolas MANOSALVA PEREZ committed May 23, 2024
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  6. Merge pull request #22 from VIB-PSB/feature/icres-based-grns 

    Feature/icres based grns
    @nicomaper
    nicomaper authored May 23, 2024
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Commits on May 24, 2024

  1. Merge pull request #23 from VIB-PSB/dev 

    iCREs-based GRN inference feature
    @nicomaper
    nicomaper authored May 24, 2024
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Commits on Jul 31, 2024

  1. Making the iCREs files public with download instructions

    Nicolas MANOSALVA PEREZ committed Jul 31, 2024
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  2. Merge pull request #24 from VIB-PSB/feature/icres-based-grns 

    Making the iCREs files public with download instructions
    @nicomaper
    nicomaper authored Jul 31, 2024
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