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More fixes and enhancements for 2.0.0#552

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szilvajuhos merged 37 commits intoSciLifeLab:masterfrom
maxulysse:1.3.0
Mar 26, 2018
Merged

More fixes and enhancements for 2.0.0#552
szilvajuhos merged 37 commits intoSciLifeLab:masterfrom
maxulysse:1.3.0

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@maxulysse maxulysse commented Mar 21, 2018 •
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  • remove UPPMAX directories from containers
  • --version is now used to define the version of the workflow
  • move version to base.config within the params --version
  • update RELEASE_CHECKLIST.md
  • add lib/SarekUtils.groovy
  • move checkParams, checkParameterList, checkParameterExistence and isAllowedParams functions into SarekUtils
  • nfRequiredVersion is now a params
  • in buildReferences.nf channels now begin by ch_, and files by f_
  • use PublishDir mode: 'link' instead of copy
  • use $PWD for default outDir to fix No results are copied to any output directory #530
  • directoryMap now contains params.outDir
  • use Nextflow support of scratch to close Use Nextflow support for /scratch instead of running directly from /scratch #539
  • update documentation
  • add CHANGELOG

maxulysse added 30 commits March 16, 2018 10:15
@maxulysse
change tag to latest
05e1d00
@maxulysse
update CHECKLIST
3cb3dde
@maxulysse
correct --outDir params
eae2ad9
@maxulysse
remove UPPMAX specific dirs
4b5157c
@maxulysse
update Checklist
2e9a6e2
@maxulysse
move all configuration into base.config + use MyUtils lib for some sh…
4a411b7 
…ared functions
@maxulysse
clean up code + use convention
c208ef6
@maxulysse
fix scripts
22d6c39
@maxulysse
update tools
0dae5de
@maxulysse
typo
492e012
@maxulysse
switch to root user
c488095
@maxulysse
fix vep user bug in vep container without changing to user root
deb6371
@maxulysse
update comments
57b9242
@maxulysse
Merge remote-tracking branch 'upstream/master' into 1.3.0
3ff02b8
@maxulysse
ennhance comments
b41eb13
@maxulysse
simplify configuration
db6dbc8
@maxulysse
use /home/max/workspace/github/Sarek instead of . to fix nf-core#530
2ec96fd
@maxulysse
use hardlink instead of copy for PublishDir
a5a176f
@maxulysse
update Checklist
b9ab0bf
@maxulysse
order tests by time
0c8b5ed
@maxulysse
remove set for single file output of process
174babe
@maxulysse
directoryMap now contains params.outDir
d0b96e6
@maxulysse
fix space missing
eea89aa
@maxulysse
typo + create function to define reference file names
507caf9
@maxulysse
directoryMap now contains params.outDir + remove old variables replac…
0757147 
…ed by parameters
@maxulysse
directoryMap now contains params.outDir + remove old variables replac…
620701d 
…ed by parameters
@maxulysse
directoryMap now contains params.outDir + remove old variables replac…
0d3fe47 
…ed by parameters
@maxulysse
directoryMap now contains params.outDir + remove old variables replac…
a084e0a 
…ed by parameters
@maxulysse
remove unused profile
f8dbb75
@maxulysse
use NF scratch support
5add69d
@maxulysse maxulysse requested a review from szilvajuhos March 23, 2018 13:01
ewels
ewels reviewed Mar 23, 2018
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Comment thread lib/MyUtils.groovy
@@ -0,0 +1,93 @@
class MyUtils {
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@ewels ewels Mar 23, 2018

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Nice, very tidy! Maybe better to call SarekUtils instead of MyUtils though, so that it's clearer in main.nf?

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@maxulysse maxulysse Mar 23, 2018

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Good idea

@szilvajuhos szilvajuhos merged commit c71d045 into SciLifeLab:master Mar 26, 2018
@maxulysse maxulysse deleted the 1.3.0 branch March 27, 2018 10:47
jherrero referenced this pull request in UCL-BLIC/Sarek_v2.2.1 Apr 11, 2019
Merge pull request nf-core#552 from MaxUlysse/1.3.0
f71c4bc 
More fixes and enhancements for 2.0.0
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Use Nextflow support for /scratch instead of running directly from /scratch No results are copied to any output directory

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@maxulysse @ewels @szilvajuhos
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