Patch release 2.3.4 #739

jfy133 · 2021-05-05T06:55:42Z

Patch release for 2.3.4.

Mostly documentation update/fixes, and a couple of bug fixes.

Only code changes are moving gzipping back into pipes for adapterremoval, and insertion of a single parameter into the bowtie2 PE command.

PR checklist

- Bumps pigz to 2.6 - removes tbb pinning

Nicer changelog, include Bowtie2

Fix pigz issues

Co-authored-by: James A. Fellows Yates <[email protected]>

update to "min_adapter_overlap" parameter for AdapterRemoval in doc

Update nextflow_schema.json

Update doc regarding bwa_index

Citation for damageprofiler

Add Bt2 --maxins

Remove social preview image to use GitHub OpenGraph

Re-add pipe to ARFixPrefix to Pigz for speed

Remove social preview image to use GitHub OpenGraph

Fix --maxins parameter in paired-end bowtie2

Dev

Version bump for 2.3.4 patch release

github-actions · 2021-05-05T06:57:11Z

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

Posted for pipeline commit 13c2f41

+| ✅ 189 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  24 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '2.3.4'
conda_env_yaml - Conda dep outdated: conda-forge::python=3.7.3, 3.9.2 available
conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.2.2, 3.3.4 available
conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=7.1, 8.1.1 available
conda_env_yaml - Conda dep outdated: conda-forge::pygments=2.6.1, 2.8.1 available
conda_env_yaml - Conda dep outdated: conda-forge::openjdk=8.0.144, 11.0.9.1 available
conda_env_yaml - Conda dep outdated: bioconda::adapterremoval=2.3.1, 2.3.2 available
conda_env_yaml - Conda dep outdated: bioconda::picard=2.22.9, 2.25.4 available
conda_env_yaml - Conda dep outdated: bioconda::samtools=1.9, 1.12 available
conda_env_yaml - Conda dep outdated: bioconda::angsd=0.933, 0.935 available
conda_env_yaml - Conda dep outdated: bioconda::gatk4=4.1.7.0, 4.2.0.0 available
conda_env_yaml - Conda dep outdated: bioconda::gatk=3.5, 3.8 available
conda_env_yaml - Conda dep outdated: bioconda::damageprofiler=0.4.9, 1.1 available
conda_env_yaml - Conda dep outdated: bioconda::bedtools=2.29.2, 2.30.0 available
conda_env_yaml - Conda dep outdated: conda-forge::libiconv=1.15, 1.16 available
conda_env_yaml - Conda dep outdated: bioconda::preseq=2.0.3, 3.1.2 available
conda_env_yaml - Conda dep outdated: bioconda::bamutil=1.0.14, 1.0.15 available
conda_env_yaml - Conda dep outdated: bioconda::pysam=0.15.4, 0.16.0 available
conda_env_yaml - Conda dep outdated: conda-forge::pandas=1.0.4, 1.2.4 available
conda_env_yaml - Conda dep outdated: bioconda::freebayes=1.3.2, 1.3.5 available
conda_env_yaml - Conda dep outdated: conda-forge::biopython=1.76, 1.78 available
conda_env_yaml - Conda dep outdated: conda-forge::xopen=0.9.0, 1.1.0 available
conda_env_yaml - Conda dep outdated: bioconda::mapdamage2=2.2.0, 2.2.1 available
conda_env_yaml - Conda dep outdated: bioconda::bbmap=38.87, 38.90 available

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.md
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: CHANGELOG.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.md
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File found: .github/markdownlint.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-eager_logo.png
files_exist - File found: bin/markdown_to_html.py
files_exist - File found: docs/images/nf-core-eager_logo.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: main.nf
files_exist - File found: environment.yml
files_exist - File found: Dockerfile
files_exist - File found: conf/base.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
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: .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: 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 found: process.container
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 process.container looks correct: nfcore/eager:2.3.4
files_unchanged - .gitattributes 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/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.md matches the template
files_unchanged - .github/markdownlint.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-eager_logo.png matches the template
files_unchanged - bin/markdown_to_html.py matches the template
files_unchanged - docs/images/nf-core-eager_logo.png matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreSchema.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .github/workflows/push_dockerhub_dev.yml matches the template
files_unchanged - .github/workflows/push_dockerhub_release.yml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - CI is building the correct docker image: docker build --no-cache . -t nfcore/eager:2.3.4
actions_ci - CI is pulling the correct docker image: docker pull nfcore/eager:dev
actions_ci - CI is tagging docker image correctly: docker tag nfcore/eager:dev nfcore/eager:2.3.4
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: 20.07.1, Config: 20.07.1
readme - README had a bioconda badge
conda_env_yaml - Conda environment name was correct (nf-core-eager-2.3.4)
conda_env_yaml - Conda dep had pinned version number: conda-forge::python=3.7.3
conda_env_yaml - Conda dep had pinned version number: conda-forge::markdown=3.2.2
conda_env_yaml - Conda dep had pinned version number: conda-forge::pymdown-extensions=7.1
conda_env_yaml - Conda dep had pinned version number: conda-forge::pygments=2.6.1
conda_env_yaml - Conda dep had pinned version number: bioconda::rename=1.601
conda_env_yaml - Conda package is the latest available: bioconda::rename=1.601
conda_env_yaml - Conda dep had pinned version number: conda-forge::openjdk=8.0.144
conda_env_yaml - Conda dep had pinned version number: bioconda::fastqc=0.11.9
conda_env_yaml - Conda package is the latest available: bioconda::fastqc=0.11.9
conda_env_yaml - Conda dep had pinned version number: bioconda::adapterremoval=2.3.1
conda_env_yaml - Conda dep had pinned version number: bioconda::adapterremovalfixprefix=0.0.5
conda_env_yaml - Conda package is the latest available: bioconda::adapterremovalfixprefix=0.0.5
conda_env_yaml - Conda dep had pinned version number: bioconda::bwa=0.7.17
conda_env_yaml - Conda package is the latest available: bioconda::bwa=0.7.17
conda_env_yaml - Conda dep had pinned version number: bioconda::picard=2.22.9
conda_env_yaml - Conda dep had pinned version number: bioconda::samtools=1.9
conda_env_yaml - Conda dep had pinned version number: bioconda::dedup=0.12.8
conda_env_yaml - Conda package is the latest available: bioconda::dedup=0.12.8
conda_env_yaml - Conda dep had pinned version number: bioconda::angsd=0.933
conda_env_yaml - Conda dep had pinned version number: bioconda::circularmapper=1.93.5
conda_env_yaml - Conda package is the latest available: bioconda::circularmapper=1.93.5
conda_env_yaml - Conda dep had pinned version number: bioconda::gatk4=4.1.7.0
conda_env_yaml - Conda dep had pinned version number: bioconda::gatk=3.5
conda_env_yaml - Conda dep had pinned version number: bioconda::qualimap=2.2.2d
conda_env_yaml - Conda package is the latest available: bioconda::qualimap=2.2.2d
conda_env_yaml - Conda dep had pinned version number: bioconda::vcf2genome=0.91
conda_env_yaml - Conda package is the latest available: bioconda::vcf2genome=0.91
conda_env_yaml - Conda dep had pinned version number: bioconda::damageprofiler=0.4.9
conda_env_yaml - Conda dep had pinned version number: bioconda::multiqc=1.10.1
conda_env_yaml - Conda package is the latest available: bioconda::multiqc=1.10.1
conda_env_yaml - Conda dep had pinned version number: bioconda::pmdtools=0.60
conda_env_yaml - Conda package is the latest available: bioconda::pmdtools=0.60
conda_env_yaml - Conda dep had pinned version number: bioconda::bedtools=2.29.2
conda_env_yaml - Conda dep had pinned version number: conda-forge::libiconv=1.15
conda_env_yaml - Conda dep had pinned version number: conda-forge::pigz=2.6
conda_env_yaml - Conda package is the latest available: conda-forge::pigz=2.6
conda_env_yaml - Conda dep had pinned version number: bioconda::sequencetools=1.4.0.6
conda_env_yaml - Conda package is the latest available: bioconda::sequencetools=1.4.0.6
conda_env_yaml - Conda dep had pinned version number: bioconda::preseq=2.0.3
conda_env_yaml - Conda dep had pinned version number: bioconda::fastp=0.20.1
conda_env_yaml - Conda package is the latest available: bioconda::fastp=0.20.1
conda_env_yaml - Conda dep had pinned version number: bioconda::bamutil=1.0.14
conda_env_yaml - Conda dep had pinned version number: bioconda::mtnucratio=0.7
conda_env_yaml - Conda package is the latest available: bioconda::mtnucratio=0.7
conda_env_yaml - Conda dep had pinned version number: bioconda::pysam=0.15.4
conda_env_yaml - Conda dep had pinned version number: bioconda::kraken2=2.1.1
conda_env_yaml - Conda package is the latest available: bioconda::kraken2=2.1.1
conda_env_yaml - Conda dep had pinned version number: conda-forge::pandas=1.0.4
conda_env_yaml - Conda dep had pinned version number: bioconda::freebayes=1.3.2
conda_env_yaml - Conda dep had pinned version number: bioconda::sexdeterrmine=1.1.2
conda_env_yaml - Conda package is the latest available: bioconda::sexdeterrmine=1.1.2
conda_env_yaml - Conda dep had pinned version number: bioconda::multivcfanalyzer=0.85.2
conda_env_yaml - Conda package is the latest available: bioconda::multivcfanalyzer=0.85.2
conda_env_yaml - Conda dep had pinned version number: bioconda::hops=0.35
conda_env_yaml - Conda package is the latest available: bioconda::hops=0.35
conda_env_yaml - Conda dep had pinned version number: conda-forge::biopython=1.76
conda_env_yaml - Conda dep had pinned version number: conda-forge::xopen=0.9.0
conda_env_yaml - Conda dep had pinned version number: bioconda::bowtie2=2.4.2
conda_env_yaml - Conda package is the latest available: bioconda::bowtie2=2.4.2
conda_env_yaml - Conda dep had pinned version number: bioconda::eigenstratdatabasetools=1.0.2
conda_env_yaml - Conda package is the latest available: bioconda::eigenstratdatabasetools=1.0.2
conda_env_yaml - Conda dep had pinned version number: bioconda::mapdamage2=2.2.0
conda_env_yaml - Conda dep had pinned version number: bioconda::bbmap=38.87
conda_dockerfile - Found all expected strings in Dockerfile file
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (143 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: push_dockerhub_dev.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: push_dockerhub_release.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

Run details

nf-core/tools version 1.13.3
Run at 2021-05-05 07:16:57

maxulysse

LGTM

maxulysse · 2021-05-05T08:01:56Z

CHANGELOG.md

+### `Deprecated`
+


Suggested change

### `Deprecated`

I tend to remove empty sections, but not sure if it's how it really should be done

I personally always carry all sections over for consistency, so will keep here. Dev choice I guess 🤷

jfy133 · 2021-05-05T11:21:17Z

Ok close enough, here we go!

jfy133 and others added 30 commits April 8, 2021 13:40

Post-release bump versions

2ab50cf

Fix pigz issues

2b9db90

- Bumps pigz to 2.6 - removes tbb pinning

Update CHANGELOG.md

150fbe8

Update CHANGELOG.md

4122f17

Update environment.yml

7ec7a80

Nicer changelog

60fbe38

Nicer changelog, include Bowtie2

Merge pull request #721 from nf-core/fix-env-pigz

6d6c5b0

Fix pigz issues

update bwa_index doc

253507e

Update nextflow_schema.json

7fe1501

Co-authored-by: James A. Fellows Yates <[email protected]>

Update nextflow_schema.json

58fb1f0

update to "min_adapter_overlap" parameter for AdapterRemoval in doc

Update main.nf

47e18a0

Update main.nf

ad448fe

Update CHANGELOG.md

2f6e3cc

Update CHANGELOG.md

cae5161

Merge pull request #727 from ashildv/dev

3ffe92e

Update nextflow_schema.json

update changelog

0e4ef9c

merge from PR

6709431

Citation for damageprofiler

aa4d0a6

Update CHANGELOG.md

806e247

Update CHANGELOG.md

bed1baf

Merge branch 'dev' into minor-doc-update

5fa6e53

Merge pull request #725 from nf-core/minor-doc-update

f1577ab

Update doc regarding bwa_index

Update CHANGELOG.md

e84cf29

Merge branch 'dev' into dmgprof-add-citation

380374c

Update CHANGELOG.md

28ac4e4

Merge branch 'dev' into re-pipe-arfixprefix

e612aad

Added --maxins for bt2

6c495df

Update CHANGELOG.md

1687722

Merge pull request #730 from nf-core/dmgprof-add-citation

b0fd5ba

Citation for damageprofiler

Merge branch 'dev' into re-pipe-arfixprefix

561ad8b

apeltzer and others added 12 commits April 26, 2021 10:24

Merge pull request #732 from nf-core/bt2-maxins

55e2eee

Add Bt2 --maxins

feat: remove social preview image to use GitHub OpenGraph

f92ac3c

Merge pull request #733 from maxulysse/dev

a6b6212

Remove social preview image to use GitHub OpenGraph

Merge pull request #731 from nf-core/re-pipe-arfixprefix

1c184aa

Re-add pipe to ARFixPrefix to Pigz for speed

feat: remove social preview image to use GitHub OpenGraph

a5c6a1e

Merge pull request #734 from maxulysse/dev

33f1b68

Remove social preview image to use GitHub OpenGraph

Fix --maxins parameter in paired-end bowtie2

4d9773b

Merge pull request #735 from charles-plessy/patch-6

ba5fd98

Fix --maxins parameter in paired-end bowtie2

Merge pull request #12 from nf-core/dev

7ba7016

Dev

Version bump for release

656e8e8

More version bumps

0cddbbf

Merge pull request #738 from jfy133/ver-bump

2e7f527

Version bump for 2.3.4 patch release

jfy133 requested a review from a team May 5, 2021 06:57

maxulysse approved these changes May 5, 2021

View reviewed changes

Update CHANGELOG.md

13c2f41

apeltzer approved these changes May 5, 2021

View reviewed changes

maxulysse reviewed May 5, 2021

View reviewed changes

jfy133 merged commit 10bfbdf into master May 5, 2021

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Patch release 2.3.4 #739

Patch release 2.3.4 #739

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Patch release 2.3.4 #739

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