nextflow-io / nf-schema

Functionality for working with pipeline and sample sheet schema files in Nextflow pipelines
https://nextflow-io.github.io/nf-schema/
Apache License 2.0
12 stars 21 forks source link

Fixes display of configFiles entries in parameter summary text #76

Closed scwatts closed 3 weeks ago

scwatts commented 4 weeks ago

Simplified operations

def a = [1, 2, 3]

def String b = a
def c = b.join(', ')

def d = a.join(', ')

println "a ${a}"
println "b ${b}"
println "c ${c}"
println "d ${d}"

Output

a [1, 2, 3]
b [1, 2, 3]
c
d 1, 2, 3
nvnieuwk commented 4 weeks ago

It seems like this broke some things in the plugin, can you take a look at it? (You can run make test to run the tests locally)

scwatts commented 3 weeks ago

Thanks for pointing that out! I've updated the fix and tests are now passing, and I confirmed the change causes config files to be shown in the parameter summary as expected after executing make install and then running example given in the corresponding issue.


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/configfilesdebug 1.0.0dev
------------------------------------------------------
Input/output options
  input      : assets/samplesheet.csv
  outdir     : output/

Core Nextflow options
  runName    : sharp_brattain
  launchDir  : /Users/stephen/temp/delete/configfiles-debug
  workDir    : /Users/stephen/temp/delete/configfiles-debug/work
  projectDir : /Users/stephen/temp/delete/configfiles-debug
  userName   : stephen
  profile    : standard
  configFiles: /Users/stephen/temp/delete/configfiles-debug/nextflow.config, /Users/stephen/temp/delete/configfiles-debug/first.config, /Users/stephen/temp/delete/configfiles-debug/second.config

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
nvnieuwk commented 3 weeks ago

Awesome, can you also update the changelog? Next version should be v2.3.0

scwatts commented 3 weeks ago

Done, and appreciate all the patience!