PR for Release 1.4 #228

apeltzer · 2018-12-12T15:05:22Z

Bump this to V1.4!

For details check out the CHANGELOG

Added bioconda badge to readme

Moved custom Institutional configs to nf-core configs on github

Added missing `local.md` to docs

The openjdk version definened in the example was not the latest anymore, so it suddenly appeared in the linting warning list and caused the linting to fail.

Update dev from master

See travis-ci/travis-ci#6069 (comment)

Attempt at making PRs fail if the CHANGELOG.md is not updated.

…onfiguration/adding_your_own.md Co-Authored-By: drpatelh <[email protected]>

Removed unused import statements

Move requests cache setup into a utils function Make cache directory and sqlite file world writeable for multi-user installations

Requests caching - multi user fix.

Co-Authored-By: apeltzer <[email protected]>

Put all input files into channels in template

Handle missing nextflow installation. See #208

See #225.

Gotta love automated testing...

Travis - Pull :dev docker image for tests.

Bumped version for 1.4 release

ewels · 2018-12-12T15:10:31Z

This pull request fixes 11 alerts when merging 9219e2b into aa947db - view on LGTM.com

fixed alerts:

11 for Unused import

Comment posted by LGTM.com

codecov-io · 2018-12-12T15:10:49Z

Codecov Report

Merging #228 into master will decrease coverage by 0.69%.
The diff coverage is 73.07%.

@@            Coverage Diff            @@
##           master     #228     +/-   ##
=========================================
- Coverage   90.87%   90.17%   -0.7%     
=========================================
  Files           8        8             
  Lines         931      936      +5     
=========================================
- Hits          846      844      -2     
- Misses         85       92      +7

Impacted Files	Coverage Δ
nf_core/create.py	`89.36% <ø> (-0.23%)`	⬇️
nf_core/download.py	`93.5% <ø> (-0.05%)`	⬇️
nf_core/lint.py	`93.31% <100%> (-0.39%)`	⬇️
nf_core/bump_version.py	`94.36% <100%> (ø)`	⬆️
nf_core/list.py	`80.32% <37.5%> (-2%)`	⬇️
nf_core/utils.py	`92.85% <84.61%> (-7.15%)`	⬇️

Continue to review full report at Codecov.

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CHANGELOG.md

* Removed remaining instances of -profile standard * Removed UPPMAX-specific appendices for installation docs.

ewels

Noticed a few minor things, made PR #229 to dev to address them.

ewels · 2018-12-12T15:13:06Z

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/installation.md

+
+## 5) Appendices

 #### Running on UPPMAX


We should probably remove this now...

Co-Authored-By: apeltzer <[email protected]>

ewels · 2018-12-12T15:27:58Z

This pull request fixes 11 alerts when merging 58bdc96 into aa947db - view on LGTM.com

fixed alerts:

11 for Unused import

Comment posted by LGTM.com

Template docs update.

ewels · 2018-12-12T15:34:30Z

This pull request fixes 11 alerts when merging 06507ce into aa947db - view on LGTM.com

fixed alerts:

11 for Unused import

Comment posted by LGTM.com

apeltzer and others added 30 commits November 22, 2018 09:58

Added bioconda badge to readme

7feb31f

Merge pull request #205 from apeltzer/add-conda-badge

3d0a6f4

Added bioconda badge to readme

Moved custom Institutional configs to nf-core configs on github

b9d9c58

Merge pull request #212 from drpatelh/dev

8706a01

Moved custom Institutional configs to nf-core configs on github

Fixed a couple of typos

fc49103

Referenced in README.md but missing from template

2dab27f

Custom configs have now been moved to nf-core/configs on github

aec3a91

Added details for adding local.md

0bce4cb

Merge pull request #214 from drpatelh/dev

f250c90

Added missing `local.md` to docs

Merge branch 'dev' into master

179e259

Fix tests

309ec50

The openjdk version definened in the example was not the latest anymore, so it suddenly appeared in the linting warning list and caused the linting to fail.

Merge branch 'master' of github.com:nf-core/tools

7c3e3a7

Merge pull request #217 from nf-core/master

9d0b367

Update dev from master

Attempt at making PRs fail if the CHANGELOG.md is not updated.

9b245f5

Fetch remotes first

c9ca1ca

See travis-ci/travis-ci#6069 (comment)

Clean up debugging statements

155dff5

Update the changelog

6411bed

Merge pull request #218 from ewels/force-changelog

1702fbd

Attempt at making PRs fail if the CHANGELOG.md is not updated.

Changed listing and added link to local installation

7293ada

Added bullet for reference genomes in line with docs README.md

fd5a1cc

Major overhaul, removal and addition of parameters

10013f2

Added a bit of info for providing custom config files

5fd3cf0

Bug-fixes and adding links to missing sections

34fdb74

Added TODO statment if parameters arent relevant

f5270e3

Fixed typo

11b776a

Added description of changes

199ac83

Update nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/c…

c74fc2d

…onfiguration/adding_your_own.md Co-Authored-By: drpatelh <[email protected]>

Removed whitespace

b94d148

Merge branch 'dev' of https://github.com/drpatelh/tools into dev

cdef837

Minor change in description for custom configs

4d687f5

sven1103 and others added 16 commits December 3, 2018 19:53

Merge pull request #220 from ewels/master

a27f13f

Removed unused import statements

Requests caching - multi user fix.

b49b3b4

Move requests cache setup into a utils function Make cache directory and sqlite file world writeable for multi-user installations

Merge pull request #221 from ewels/cache_perm_fix

0ef2a29

Requests caching - multi user fix.

Add Channel handling of input files

b31e9c8

Add changelog

e0ee8ba

Mini bump to get PR to buildagain

f8eeeb5

Update nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf

503813b

Co-Authored-By: apeltzer <[email protected]>

Update nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf

46828e6

Co-Authored-By: apeltzer <[email protected]>

Merge pull request #223 from apeltzer/dev

62abdf9

Put all input files into channels in template

Handle missing nextflow installation. See #208

93ed1e2

Merge pull request #224 from ewels/master

50ede3b

Handle missing nextflow installation. See #208

Travis - Pull :dev docker image for tests.

a4aac1c

See #225.

Updated a few docker tag statements that I had missed.

a916d32

Gotta love automated testing...

Merge pull request #226 from ewels/master

3a450c5

Travis - Pull :dev docker image for tests.

Bumped version for 1.4 release

826818f

Merge pull request #227 from ewels/master

9219e2b

Bumped version for 1.4 release

apeltzer requested a review from a team December 12, 2018 15:05

sven1103 requested changes Dec 12, 2018

View reviewed changes

CHANGELOG.md Outdated Show resolved Hide resolved

Template docs update.

141a63c

* Removed remaining instances of -profile standard * Removed UPPMAX-specific appendices for installation docs.

ewels requested changes Dec 12, 2018

View reviewed changes

sven1103 and others added 2 commits December 12, 2018 16:21

Update CHANGELOG.md

58bdc96

Co-Authored-By: apeltzer <[email protected]>

Goddam changelog updates

636d050

Merge pull request #229 from ewels/master

06507ce

Template docs update.

ewels approved these changes Dec 12, 2018

View reviewed changes

sven1103 approved these changes Dec 12, 2018

View reviewed changes

apeltzer merged commit 54e233a into master Dec 12, 2018

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