PR for Maintenance Release 1.1.1 #32

apeltzer · 2020-10-14T18:45:50Z

This is a maintenance release mainly used to fix issues with time-outing tbl2asn (in prokka).

Adds some updates to tools used (where possible) - dependencies are now in larger fractions in separate containers from biocontainers to get things working more smoothly.
Adds JSON Schema for Workflow to launch pipeline more easily (see here

PR checklist

This comment contains a description of changes (with reason)
If you've fixed a bug or added code that should be tested, add tests!
If necessary, also make a PR on the nf-core/bacass branch on the nf-core/test-datasets repo
Ensure the test suite passes (nextflow run . -profile test,docker).
Make sure your code lints (nf-core lint .).
Documentation in docs is updated
CHANGELOG.md is updated
README.md is updated

Learn more about contributing: https://github.com/nf-core/bacass/tree/master/.github/CONTRIBUTING.md

Add social preview image

Dev

Fix Zenodo DOI in readme

…ntainers

github-actions · 2020-10-14T18:46:52Z

`nf-core lint` overall result: Passed ✅

Updated for pipeline commit 9485619

+| ✅ 101 tests passed       |+
!| ❗  7 tests had warnings |!
-| ❌  0 tests failed       |-

Details

❗ Test warnings:

Test #4 - Config manifest.version should end in dev: '1.1.1'
Test #5 - GitHub Actions AWS full test should test full datasets: /home/runner/work/bacass/bacass/.github/workflows/awsfulltest.yml
Test #8 - Conda package is not latest available: python=3.7.3, 3.9.0 available
Test #8 - Conda package is not latest available: conda-forge::markdown=3.3, 3.3.3 available
Test #8 - Conda package is not latest available: conda-forge::pygments=2.7.1, 2.7.2 available
Test #8 - Conda package is not latest available: kraken2=2.0.9beta, 2.1.0 available
Test #8 - Conda package is not latest available: canu=2.0, 2.1.1 available

✅ Tests passed:

Test #1 - File found: nextflow.config
Test #1 - File found: nextflow_schema.json
Test #1 - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
Test #1 - File found: README.md
Test #1 - File found: CHANGELOG.md
Test #1 - File found: docs/README.md
Test #1 - File found: docs/output.md
Test #1 - File found: docs/usage.md
Test #1 - File found: .github/workflows/branch.yml
Test #1 - File found: .github/workflows/ci.yml
Test #1 - File found: .github/workflows/linting.yml
Test #1 - File found: main.nf
Test #1 - File found: environment.yml
Test #1 - File found: Dockerfile
Test #1 - File found: conf/base.config
Test #1 - File found: .github/workflows/awstest.yml
Test #1 - File found: .github/workflows/awsfulltest.yml
Test #1 - File not found check: Singularity
Test #1 - File not found check: parameters.settings.json
Test #1 - File not found check: bin/markdown_to_html.r
Test #1 - File not found check: .travis.yml
Test #3 - Licence check passed
Test #2 - Dockerfile check passed
Test #4 - Config variable found: manifest.name
Test #4 - Config variable found: manifest.nextflowVersion
Test #4 - Config variable found: manifest.description
Test #4 - Config variable found: manifest.version
Test #4 - Config variable found: manifest.homePage
Test #4 - Config variable found: timeline.enabled
Test #4 - Config variable found: trace.enabled
Test #4 - Config variable found: report.enabled
Test #4 - Config variable found: dag.enabled
Test #4 - Config variable found: process.cpus
Test #4 - Config variable found: process.memory
Test #4 - Config variable found: process.time
Test #4 - Config variable found: params.outdir
Test #4 - Config variable found: params.input
Test #4 - Config variable found: manifest.mainScript
Test #4 - Config variable found: timeline.file
Test #4 - Config variable found: trace.file
Test #4 - Config variable found: report.file
Test #4 - Config variable found: dag.file
Test #4 - Config variable found: process.container
Test #4 - Config variable (correctly) not found: params.version
Test #4 - Config variable (correctly) not found: params.nf_required_version
Test #4 - Config variable (correctly) not found: params.container
Test #4 - Config variable (correctly) not found: params.singleEnd
Test #4 - Config variable (correctly) not found: params.igenomesIgnore
Test #4 - Config timeline.enabled had correct value: true
Test #4 - Config report.enabled had correct value: true
Test #4 - Config trace.enabled had correct value: true
Test #4 - Config dag.enabled had correct value: true
Test #4 - Config manifest.name began with nf-core/
Test #4 - Config variable manifest.homePage began with https://github.com/nf-core/
Test #4 - Config dag.file ended with .svg
Test #4 - Config variable manifest.nextflowVersion started with >= or !>=
Test #4 - Config process.container looks correct: nfcore/bacass:1.1.1
Test #5 - GitHub Actions 'branch' workflow is triggered for PRs to master: /home/runner/work/bacass/bacass/.github/workflows/branch.yml
Test #5 - GitHub Actions 'branch' workflow looks good: /home/runner/work/bacass/bacass/.github/workflows/branch.yml
Test #5 - GitHub Actions CI is triggered on expected events: /home/runner/work/bacass/bacass/.github/workflows/ci.yml
Test #5 - CI is building the correct docker image: docker build --no-cache . -t nfcore/bacass:1.1.1
Test #5 - CI is pulling the correct docker image: docker pull nfcore/bacass:dev
Test #5 - CI is tagging docker image correctly: docker tag nfcore/bacass:dev nfcore/bacass:1.1.1
Test #5 - Continuous integration checks minimum NF version: /home/runner/work/bacass/bacass/.github/workflows/ci.yml
Test #5 - GitHub Actions linting workflow is triggered on PR and push: /home/runner/work/bacass/bacass/.github/workflows/linting.yml
Test #5 - Continuous integration runs Markdown lint Tests: /home/runner/work/bacass/bacass/.github/workflows/linting.yml
Test #5 - Continuous integration runs nf-core lint Tests: /home/runner/work/bacass/bacass/.github/workflows/linting.yml
Test #5 - GitHub Actions AWS test is triggered on workflow_dispatch: /home/runner/work/bacass/bacass/.github/workflows/awstest.yml
Test #5 - GitHub Actions AWS full test is triggered only on published release and workflow_dispatch: /home/runner/work/bacass/bacass/.github/workflows/awsfulltest.yml
Test #6 - README Nextflow minimum version badge matched config. Badge: 19.10.0, Config: 19.10.0
Test #6 - README had a bioconda badge
Test #8 - Conda environment name was correct (nf-core-bacass-1.1.1)
Test #8 - Conda dependency had pinned version number: python=3.7.3
Test #8 - Conda dependency had pinned version number: conda-forge::markdown=3.3
Test #8 - Conda dependency had pinned version number: conda-forge::pymdown-extensions=8.0.1
Test #8 - Conda package is latest available: conda-forge::pymdown-extensions=8.0.1
Test #8 - Conda dependency had pinned version number: conda-forge::pygments=2.7.1
Test #8 - Conda dependency had pinned version number: fastqc=0.11.9
Test #8 - Conda package is latest available: fastqc=0.11.9
Test #8 - Conda dependency had pinned version number: multiqc=1.9
Test #8 - Conda package is latest available: multiqc=1.9
Test #8 - Conda dependency had pinned version number: skewer=0.2.2
Test #8 - Conda package is latest available: skewer=0.2.2
Test #8 - Conda dependency had pinned version number: kraken2=2.0.9beta
Test #8 - Conda dependency had pinned version number: conda-forge::parallel=20200922
Test #8 - Conda package is latest available: conda-forge::parallel=20200922
Test #8 - Conda dependency had pinned version number: miniasm=0.3_r179
Test #8 - Conda package is latest available: miniasm=0.3_r179
Test #8 - Conda dependency had pinned version number: racon=1.4.13
Test #8 - Conda package is latest available: racon=1.4.13
Test #8 - Conda dependency had pinned version number: minimap2=2.17
Test #8 - Conda package is latest available: minimap2=2.17
Test #8 - Conda dependency had pinned version number: canu=2.0
Test #8 - Conda dependency had pinned version number: h5py=2.10.0
Test #8 - Conda package is latest available: h5py=2.10.0
Test #9 - Found all expected strings in Dockerfile file
Test #12 - Name adheres to nf-core convention
Test #13 - Did not find any cookiecutter template strings (55 files)
Test #14 - Schema lint passed
Test #14 - Schema title + description lint passed
Test #15 - Schema matched params returned from nextflow config

Run details:

nf-core/tools version 1.11
Run at 2020-11-05 10:21:49

.github/markdownlint.yml

.github/workflows/awsfulltest.yml

CHANGELOG.md

conf/base.config

conf/test_full.config

docs/containers.md

docs/usage.md

nextflow.config

Important! Template update for nf-core/tools v1.11

main.nf

assets/nf-core-bacass_logo.png

nextflow.config

ggabernet

Looks good to me!

apeltzer · 2020-11-05T10:06:39Z

Adressed your points @maxulysse / @jfy133

CHANGELOG.md

apeltzer and others added 30 commits December 13, 2019 14:51

Bump to 1.2.0dev

e9aa56e

Update README.md

f51238c

Merge branch 'dev' into readme-zenodo-fix

b63ac86

add social preview image

8f16309

add social preview images

7d54838

update CHANGELOG

1a70e8b

Template update for nf-core/tools version 1.9

12fe86e

Merge pull request #20 from MaxUlysse/dev

b6861c0

Add social preview image

Add test_dfast profile, uses dfast instead of prokka

2b5cb2e

Add description in test_dfast.config

e984dbf

Merge pull request #22 from angelovangel/dev

232d18d

Dev

Template update for nf-core/tools version 1.10.1

2d5fcc3

Template update for nf-core/tools version 1.10.2

2d14ee9

Merge pull request #19 from nf-core/readme-zenodo-fix

528c1c5

Fix Zenodo DOI in readme

Merge remote-tracking branch 'upstream/TEMPLATE' into dev

ff52fd7

Minimal update

4b3a79f

Merge branch 'dev' of https://github.com/nf-core/bacass into dev

3dcedf9

Some updates to changelog

cf9d064

Add this properly

5c63c37

Fix linting issues

ea35aad

Add conda disclaimer

f2720e8

Minor adjustments

f1fe658

add schema + publish dir mode

f50bdaa

Adding in first attempts to replace one container with multiple bioco…

5867552

…ntainers

Fix environments appropriately

9ab889b

Much cleaner containers

e8ba1c9

Follow drpatelh style

fd2c4df

version.txt everywhere

4c48b62

Adding in harshils magic

8dea1bf

Nicer schema

cc5c749

Fixing canu issues now

33b5e09

apeltzer requested a review from a team October 14, 2020 18:45

apeltzer added 2 commits October 14, 2020 20:47

Bump to 1.1.1 for release

0494852

Changelog updated

6aa5b25

jfy133 reviewed Oct 15, 2020

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jfy133 approved these changes Oct 15, 2020

View reviewed changes

apeltzer and others added 8 commits October 18, 2020 12:08

Adjust changes from review

9579dab

Template update for nf-core/tools version 1.11

407380f

Merge branch 'dev' into TEMPLATE

2d11a37

Merge pull request #33 from nf-core/TEMPLATE

b59102c

Important! Template update for nf-core/tools v1.11

Adjust handling of labels vs names

ad69e1b

Fix label issue

2de1888

Fix png issue

5c86fff

Fix tests

188b18d

apeltzer commented Nov 4, 2020

View reviewed changes

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Update main.nf

1b64e6e

apeltzer commented Nov 5, 2020

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main.nf Show resolved Hide resolved

Update main.nf

4f26506

jfy133 reviewed Nov 5, 2020

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jfy133 requested changes Nov 5, 2020

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ggabernet approved these changes Nov 5, 2020

View reviewed changes

Fix last two issues / comments

d2913e8

apeltzer requested a review from jfy133 November 5, 2020 10:06

jfy133 approved these changes Nov 5, 2020

View reviewed changes

Fix issue with multiqc config

e7da941

apeltzer commented Nov 5, 2020

View reviewed changes

CHANGELOG.md Outdated Show resolved Hide resolved

Update CHANGELOG.md

9485619

apeltzer merged commit 4500b3b into master Nov 5, 2020

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PR for Maintenance Release 1.1.1 #32

PR for Maintenance Release 1.1.1 #32

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❗ Test warnings:

✅ Tests passed:

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PR for Maintenance Release 1.1.1 #32

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apeltzer commented Oct 14, 2020

PR checklist

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nf-core lint overall result: Passed ✅

❗ Test warnings:

✅ Tests passed:

Run details:

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github-actions bot commented Oct 14, 2020 •

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`nf-core lint` overall result: Passed ✅