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SystemsGenetics / GEMmaker

A workflow for construction of Gene Expression count Matrices (GEMs). Useful for Differential Gene Expression (DGE) analysis and Gene Co-Expression Network (GCN) construction
https://gemmaker.readthedocs.io/en/latest/
MIT License
33 stars 16 forks source link

`baseDir` has been deprecated #271

Open JohnHadish opened 1 year ago

JohnHadish commented 1 year ago

Description of the bug

GEMmaker uses the script implicit variable baseDir in several of its example scripts. As of 20.04.0 Nextflow has deprecated baseDir and instead prefers user to use projectDir and launchDir. https://www.nextflow.io/docs/latest/script.html

We already use the projectDir nomenclature when reporting directories at the beginning of GEMmaker. baseDir references should be changed everywhere within GEMmaker.

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  systemsgenetics/gemmaker v2.1.0dev
------------------------------------------------------
Core Nextflow options
  revision                  : gem_fix
  runName                   : angry_thompson
  containerEngine           : singularity
  launchDir                 : /scidas/unmigrated/John/GEMmaker_270
  workDir                   : /scidas/unmigrated/John/GEMmaker_270/work
  projectDir                : /home/john.hadish/.nextflow/assets/systemsgenetics/gemmaker
  userName                  : john.hadish
  profile                   : kamiak,singularity
  configFiles               : /home/john.hadish/.nextflow/assets/systemsgenetics/gemmaker/nextflow.config, /scidas/unmigrated/John/GEMmaker_270/nextflow.config

Command used and terminal output

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Relevant files

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System information

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