Add check to lint for deprecated syntax

[senthil10]

nextflow had an update in syntax for process specific configuration. Idea is to encourage the new syntax (withName: processName) as it is more flexible. So point out the deprecated syntax ($processName) in warning while linting.

It is fairly easy now (thanks to how nextflow lists the current user defined configuration). For instance

With deprecated syntax:

[u'process.$makeHISATindex.cpus', u'process.$workflow_summary_mqc.cache', u'process.$makeSTARindex.time', u'process.$star.time', u'process.$hisat2Align.time']

With cool new syntax:

[u"process. 'withName:makeHISATindex'.cpus", u"process. 'withName:workflow_summary_mqc'.cache", u"process. 'withName:makeSTARindex'.time", u"process. 'withName:star'.time", u"process. 'withName:hisat2Align'.time"]

[codecov-io]

Codecov Report

Merging #104 into dev will increase coverage by 0.03%.
The diff coverage is 100%.

@@            Coverage Diff            @@
##             dev     #104      +/-   ##
=========================================
+ Coverage   91.7%   91.73%   +0.03%     
=========================================
  Files          7        7              
  Lines        687      690       +3     
=========================================
+ Hits         630      633       +3     
  Misses        57       57

Impacted Files	Coverage Δ
nf_core/lint.py	97.68% <100%> (+0.02%)	⬆️

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[senthil10]

Ran a local test with my old version for rnaseq package and after @apeltzer have fixed old syntax in PR #51

Lint on old syntax

$ nf-core lint /Users/senthilkumar.panneerselvam/opt/rnaseq

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

Running pipeline tests  [#####################---------------]   60%  0d 00:00:01  'check_ci_confiRunning pipeline tests  [#########################-----------]   70%  0d 00:00:01  'check_readme' Running pipeline tests  [############################--------]   80%  0d 00:00:01  'check_conda_enRunning pipeline tests  [################################----]   90%  0d 00:00:02  'check_conda_doRunning pipeline tests  [####################################]  100%  'check_conda_singularityfileRunning pipeline tests  [####################################]  100%  None

INFO: ===========
 LINTING RESULTS
=================
  80 tests passed  21 tests had warnings   0 tests failed

WARNING: Test Warnings:
  http://nf-co.re/errors#4: Process configuration is done with deprecated_syntax: process.$makeHISATindex
  http://nf-co.re/errors#4: Process configuration is done with deprecated_syntax: process.$get_software_versions
  http://nf-co.re/errors#4: Process configuration is done with deprecated_syntax: process.$hisat2Align
  http://nf-co.re/errors#4: Process configuration is done with deprecated_syntax: process.$preseq
  http://nf-co.re/errors#4: Process configuration is done with deprecated_syntax: process.$makeSTARindex
  http://nf-co.re/errors#4: Process configuration is done with deprecated_syntax: process.$fastqc
  http://nf-co.re/errors#4: Process configuration is done with deprecated_syntax: process.$hisat2_sortOutput
  http://nf-co.re/errors#4: Process configuration is done with deprecated_syntax: process.$multiqc
  http://nf-co.re/errors#4: Process configuration is done with deprecated_syntax: process.$star
  http://nf-co.re/errors#4: Process configuration is done with deprecated_syntax: process.$genebody_coverage
  http://nf-co.re/errors#4: Process configuration is done with deprecated_syntax: process.$sample_correlation
  http://nf-co.re/errors#4: Process configuration is done with deprecated_syntax: process.$markDuplicates
  http://nf-co.re/errors#4: Process configuration is done with deprecated_syntax: process.$dupradar
  http://nf-co.re/errors#4: Process configuration is done with deprecated_syntax: process.$rseqc
  http://nf-co.re/errors#4: Process configuration is done with deprecated_syntax: process.$trim_galore
  http://nf-co.re/errors#4: Process configuration is done with deprecated_syntax: process.$workflow_summary_mqc
  http://nf-co.re/errors#8: Conda package is not latest available: trim-galore=0.4.5, 0.5.0 available
  http://nf-co.re/errors#8: Conda package is not latest available: picard=2.18.7, 2.18.11 available
  http://nf-co.re/errors#8: Conda package is not latest available: samtools=1.8, 1.9 available
  http://nf-co.re/errors#8: Conda package is not latest available: subread=1.6.1, 1.6.2 available
  http://nf-co.re/errors#8: Conda package is not latest available: multiqc=1.5, 1.6 available

Lint on new syntax

$ nf-core lint /Users/senthilkumar.panneerselvam/Downloads/rnaseq

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

Running pipeline tests  [#####################---------------]   60%  0d 00:00:01  'check_ci_confiRunning pipeline tests  [#########################-----------]   70%  0d 00:00:01  'check_readme' Running pipeline tests  [############################--------]   80%  0d 00:00:01  'check_conda_enRunning pipeline tests  [################################----]   90%  0d 00:00:02  'check_conda_doRunning pipeline tests  [####################################]  100%  'check_conda_singularityfileRunning pipeline tests  [####################################]  100%  None

INFO: ===========
 LINTING RESULTS
=================
  80 tests passed   5 tests had warnings   0 tests failed

WARNING: Test Warnings:
  http://nf-co.re/errors#8: Conda package is not latest available: trim-galore=0.4.5, 0.5.0 available
  http://nf-co.re/errors#8: Conda package is not latest available: picard=2.18.7, 2.18.11 available
  http://nf-co.re/errors#8: Conda package is not latest available: samtools=1.8, 1.9 available
  http://nf-co.re/errors#8: Conda package is not latest available: subread=1.6.1, 1.6.2 available
  http://nf-co.re/errors#8: Conda package is not latest available: multiqc=1.5, 1.6 available

[apeltzer]

Nice work! I think this can go in :-)