Release 2.0.0 #124

ggabernet · 2021-12-16T16:08:42Z

Prepare release 2.0

PR checklist

Bump all versions to 2.0, and changelog update date
This comment contains a description of changes (with reason)
CHANGELOG.md is updated
If you've fixed a bug or added code that should be tested, add tests!
Documentation in docs is updated
If necessary, also make a PR on the nf-core/epitopeprediction branch on the nf-core/test-datasets repo

Merging template updates

Add NetMHC tool dependencies ahead of integration

Bump version to 1.2.0dev

Co-authored-by: Christopher Mohr <christopher.mohr@uni-tuebingen.de>

Important! Template update for nf-core/tools v1.13.3

ggabernet

Just went over it and it looks good to me (but can't approve as I'm the PR author).

Just had a small comment of formatting

CHANGELOG.md

workflows/epitopeprediction.nf

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

lib/WorkflowEpitopeprediction.groovy

modules.json

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

christopher-mohr

Just found some minor things that could be changed.

.nf-core.yml

CHANGELOG.md

CITATIONS.md

subworkflows/local/input_check.nf

Co-authored-by: Christopher Mohr <christopher.mohr@uni-tuebingen.de>

CITATIONS.md

remove fastqc module

christopher-mohr

LGTM

github-actions · 2021-12-21T12:24:10Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 251afac

+| ✅ 139 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '2.0.0'

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .markdownlint.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-epitopeprediction_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-epitopeprediction_logo_light.png
files_exist - File found: docs/images/nf-core-epitopeprediction_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreSchema.groovy
files_exist - File found: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yaml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowEpitopeprediction.groovy
files_exist - File found: modules.json
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: docs/images/nf-core-epitopeprediction_logo.png
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.show_hidden_params
nextflow_config - Config variable found: params.schema_ignore_params
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.version
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .svg
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
files_unchanged - .gitattributes matches the template
files_unchanged - .markdownlint.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-epitopeprediction_logo_light.png matches the template
files_unchanged - docs/images/nf-core-epitopeprediction_logo_light.png matches the template
files_unchanged - docs/images/nf-core-epitopeprediction_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreSchema.groovy matches the template
files_unchanged - lib/NfcoreTemplate.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - assets/multiqc_config.yaml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 21.10.3, Config: 21.10.3
readme - README Nextflow minimum version in Quick Start section matched config. README: 21.10.3, Config: 21.10.3
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (89 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json

Run details

nf-core/tools version 2.2
Run at 2021-12-21 12:04:33

nf-core-bot and others added 30 commits October 27, 2020 09:25

Template update for nf-core/tools version 1.11

2b760e8

Template update for nf-core/tools version 1.12

4b9d74a

Template update for nf-core/tools version 1.12.1

11f2569

Merged changes from nf-core template

3bbe848

Merge pull request #70 from lkuchenb/merging-template-updates

e945bb1

Merging template updates

Make alleles channels value channels

22cba8f

Add netmhc tool family dependencies

303f9ef

Merge pull request #72 from lkuchenb/add/netmhcdeps

23e0762

Add NetMHC tool dependencies ahead of integration

Bump version to 1.2.0dev

247b783

Merge pull request #74 from nf-core/versionBump

243fafe

Bump version to 1.2.0dev

Make toolname comparison case insensitive

dfdd78b

Add netmhc tool family support to the pipeline

a188cdc

Update changelog

440723f

Add contribution to README file

ef5c848

Add CI tests for NetMHC family tools

af9c521

Update docs for NetMHC integration

d66ef96

Apply suggestions from code review

67bce22

Co-authored-by: Christopher Mohr <christopher.mohr@uni-tuebingen.de>

Template update for nf-core/tools version 1.13

0786950

Template update for nf-core/tools version 1.13.1

a9863a2

Template update for nf-core/tools version 1.13.2

5c391d6

Template update for nf-core/tools version 1.13.3

5886199

Merge branch 'dev' into nf-core-template-merge-1.13.3

185e7c3

Remove param name

8371337

Change values of mhc_class param to integer values

048db96

Remove input from required params

4915129

Move env block in aws ymls, remove R from Dockerfile

c10926d

Remove input parameter from schema_ignore_params

9d4bbb5

Merge pull request #79 from nf-core/nf-core-template-merge-1.13.3

7ddc322

Important! Template update for nf-core/tools v1.13.3

Threshold customization and color fixes

366efc0

Minor change of the pipeline schema

6543537

ggabernet changed the title ~~Release 2.0~~ Release 2.0.0 Dec 21, 2021

ggabernet commented Dec 21, 2021

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Update CHANGELOG.md

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Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

marissaDubbelaar approved these changes Dec 21, 2021

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Update workflows/epitopeprediction.nf

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Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

christopher-mohr reviewed Dec 21, 2021

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Update CITATIONS.md

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Co-authored-by: Christopher Mohr <christopher.mohr@uni-tuebingen.de>

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ggabernet and others added 2 commits December 21, 2021 11:18

Update CHANGELOG.md
E85D

e6189b6

Co-authored-by: Christopher Mohr <christopher.mohr@uni-tuebingen.de>

Update subworkflows/local/input_check.nf

82b508b

Co-authored-by: Christopher Mohr <christopher.mohr@uni-tuebingen.de>

christopher-mohr reviewed Dec 21, 2021

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ggabernet and others added 4 commits December 21, 2021 12:39

remove fastqc module

22d2fa5

update worflowepitopeprediction

f4f457c

remove lint config

fc2ff4d

Merge pull request #129 from ggabernet/review-comments

251afac

remove fastqc module

christopher-mohr approved these changes Dec 21, 2021

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This was referenced Dec 21, 2021

Alter the tests so that a sample sheet can be used as input instead of one file #103

Closed

Template update for nf-core/tools v2.1 #100

Closed

nfcore module: cat (mergeFastas) #98

Closed

christopher-mohr approved these changes Dec 21, 2021

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christopher-mohr merged commit 1afbbf1 into master Dec 21, 2021

ggabernet mentioned this pull request Dec 21, 2021

Implementation of the sample sheet in the pipeline #102

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Release 2.0.0 #124

Release 2.0.0 #124

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❗ Test warnings:

✅ Tests passed:

Run details

Release 2.0.0 #124

Release 2.0.0 #124

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

`nf-core lint` overall result: Passed ✅ ⚠️