Release 2.9.0 #725

d4straub · 2024-03-28T07:24:31Z

This is release 2.9.0.

Potential problem:
For a new software I produced a container and deposited it at dockerhub. The processes that use that software are doing so with container 'docker.io/d4straub/pipesidle:0.1.0-beta'. My proposal to put the tool (pypi packaged) to conda was rejected by the developer of said tool. I generated the container with Dockerfile & environment.yml. Maybe there is a better solution to that?

Changes are:

added multiple regions analysis (including 5R / SMURF / q2-sidle), for that the meta map was extended and several new processes were added
Template update 2.11 to 2.13.1, that might be the majority of file changes
Plethora of bug fixes, for details see CHANGELOG.

PR checklist

bump-version 2.9.0dev

Merging template updates 2.12

Fix README

Added --save_intermediates

…ltiple-regions-analysis

Export all process software versions

…-modules

Update nf-core modules, DADA2, and Phyloseq

Update documentation

bump version to 2.9.0

github-actions · 2024-03-28T07:27:07Z

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

Posted for pipeline commit 4707d38

+| ✅ 190 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.9.0
readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
nextflow_config - Config default ignored: params.report_template
nextflow_config - Config default ignored: params.report_css
nextflow_config - Config default ignored: params.report_logo
files_unchanged - File ignored due to lint config: .gitattributes
actions_ci - actions_ci

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.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: 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-ampliseq_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-ampliseq_logo_light.png
files_exist - File found: docs/images/nf-core-ampliseq_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: main.nf
files_exist - File found: assets/multiqc_config.yml
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 found: modules.json
files_exist - File found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: .nf-core.yaml
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-ampliseq_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/WorkflowAmpliseq.groovy
files_exist - File not found check: lib/nfcore_external_java_deps.jar
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.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
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.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 variable (correctly) not found: params.enable_conda
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 .html
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
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.extension= /*_R{1,2}_001.fastq.gz
nextflow_config - Config default value correct: params.min_read_counts= 1
nextflow_config - Config default value correct: params.cutadapt_min_overlap= 3
nextflow_config - Config default value correct: params.cutadapt_max_error_rate= 0.1
nextflow_config - Config default value correct: params.trunc_qmin= 25
nextflow_config - Config default value correct: params.trunc_rmin= 0.75
nextflow_config - Config default value correct: params.max_ee= 2
nextflow_config - Config default value correct: params.min_len= 50
nextflow_config - Config default value correct: params.sample_inference= independent
nextflow_config - Config default value correct: params.vsearch_cluster_id= 0.97
nextflow_config - Config default value correct: params.orf_start= 1
nextflow_config - Config default value correct: params.stop_codons= TAA,TAG
nextflow_config - Config default value correct: params.dada_ref_taxonomy= silva=138
nextflow_config - Config default value correct: params.pplace_alnmethod= hmmer
nextflow_config - Config default value correct: params.kraken2_confidence= 0.0
nextflow_config - Config default value correct: params.cut_its= none
nextflow_config - Config default value correct: params.its_partial= 0
nextflow_config - Config default value correct: params.exclude_taxa= mitochondria,chloroplast
nextflow_config - Config default value correct: params.min_frequency= 1
nextflow_config - Config default value correct: params.min_samples= 1
nextflow_config - Config default value correct: params.diversity_rarefaction_depth= 500
nextflow_config - Config default value correct: params.ancom_sample_min_count= 1
nextflow_config - Config default value correct: params.tax_agglom_min= 2
nextflow_config - Config default value correct: params.tax_agglom_max= 6
nextflow_config - Config default value correct: params.report_title= Summary of analysis results
nextflow_config - Config default value correct: params.seed= 100
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
files_unchanged - .prettierrc.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-ampliseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-ampliseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-ampliseq_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
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 Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (345 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/tsv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - 'assets/multiqc_config.yml' contains report_section_order
multiqc_config - 'assets/multiqc_config.yml' contains export_plots
multiqc_config - 'assets/multiqc_config.yml' contains report_comment
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.13.1
Run at 2024-04-02 13:30:59

erikrikarddaniel

That's a lot of files. Looks fine.
The container question sounds a bit like an application of "Wave", but I don't know.

Co-authored-by: Júlia Mir Pedrol <[email protected]>

fix Download Pipeline Workflow

.editorconfig

.github/workflows/release-announcements.yml

docs/usage.md

modules/local/sidle_taxrecon.nf

modules/local/sidle_trim.nf

nextflow.config

nextflow_schema.json

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Update nextflowschema

Retrieve Sidle container from quay.io/nf-core instead of docker.io/d4straub

d4straub · 2024-04-03T08:57:04Z

Unfortunately the AWS full test run failed, will re-try and then troubleshoot.
edit: ok the run now succeeded, so seems fine after all.

d4straub and others added 30 commits January 16, 2024 16:16

bump-version 2.9.0dev

e89a674

Merge pull request #692 from d4straub/bump-version-2.9.0dev

2da3147

bump-version 2.9.0dev

Template update for nf-core/tools version 2.12

0d8dce4

template update 2.12

1d3c72d

fix indent and trailing whitespace

d19bdac

fix software versions in nf.test.snap

e0f0e76

fix prettier

ae32e2c

fix linting: ignore params.report_*

fe61543

fix prettier

039ca64

update subworkflow fasta_newick_epang_gappa

93a5869

Merge pull request #697 from d4straub/merging-template-updates-2.12

bc1a10e

Merging template updates 2.12

fix README badges

bbd5518

update CHANGELOG

37bf03f

fix typo

effb048

add --save_intermediates

376c2de

fix unused line

5fa1d1d

move primers to meta map

117e426

Merge pull request #699 from d4straub/fix-readme-and-nextflow_schema

2aa390c

Fix README

apply harshil alignment

739ccbd

Merge pull request #700 from d4straub/export-more-qza

2a23b1b

Added --save_intermediates

Merge branch 'dev' of https://github.com/nf-core/ampliseq into add-mu…

c26cbac

…ltiple-regions-analysis

process regions with --input_mutiregion

3f16376

fix when no primers are given

45fefd4

produce per-region ASV tables and fasta

715ae05

adjust container and input

0f04676

add SIDLE workflow from d4straub/pipesidle

aa1ff5a

add sidle reference taxonomy entries & custom input

afbb18f

fix prettier

a8bc971

plugin sidle output to downstream analysis

0185e0c

--sidle_ref_taxonomy greengenes works

5b4d4d0

d4straub and others added 12 commits March 26, 2024 16:33

Merge pull request #719 from d4straub/export-all-versions

0c24ff3

Export all process software versions

Merge branch 'dev' of https://github.com/nf-core/ampliseq into update…

717aa49

…-modules

Merge pull request #720 from d4straub/update-modules

43378b5

Update nf-core modules, DADA2, and Phyloseq

update params docs

a7609e0

re-do workflow figure

9c7f78c

update CHENGALOG

e575b85

improve figure

b3af0be

adjust figure

6f0b65a

Merge pull request #723 from d4straub/update-param-docu-2.9.0

db4cc0a

Update documentation

bump version to 2.9.0

3b0ea74

fix typo

d6cf941

Merge pull request #724 from d4straub/bump-version-2.9.0

08db42e

bump version to 2.9.0

erikrikarddaniel approved these changes Mar 28, 2024

View reviewed changes

d4straub and others added 3 commits March 28, 2024 10:57

fix Download Pipeline Workflow

8a0f5f2

Apply suggestions from code review

1c5ea7c

Co-authored-by: Júlia Mir Pedrol <[email protected]>

Merge pull request #726 from d4straub/fix-Download-Pipeline-Workflow

3f2f466

fix Download Pipeline Workflow

mashehu approved these changes Mar 29, 2024

View reviewed changes

d4straub and others added 5 commits April 2, 2024 08:58

Apply suggestions from code review

a060f2f

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Update nextflow.config

53cb658

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Fix linting in release-announcements.yml

4a11f03

add pattern to sidle_ref_tree_custom

92b3984

update CHANGELOG

c9def1d

d4straub mentioned this pull request Apr 2, 2024

Update nextflowschema #728

Merged

11 tasks

d4straub and others added 4 commits April 2, 2024 11:25

fix pattern

066df3d

Merge pull request #728 from d4straub/update-nextflowschema

b68e479

Update nextflowschema

retrieve sidle container from quay.io/nf-core

b42e8f0

Merge pull request #729 from d4straub/pipesidle-container

4707d38

Retrieve Sidle container from quay.io/nf-core instead of docker.io/d4straub

d4straub merged commit 717abb8 into master Apr 3, 2024
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Release 2.9.0 #725

Release 2.9.0 #725

d4straub commented Mar 28, 2024 •

edited

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github-actions bot commented Mar 28, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

erikrikarddaniel left a comment

d4straub commented Apr 3, 2024 •

edited

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Release 2.9.0 #725

Release 2.9.0 #725

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d4straub commented Mar 28, 2024 • edited Loading

PR checklist

github-actions bot commented Mar 28, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

erikrikarddaniel left a comment

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d4straub commented Apr 3, 2024 • edited Loading

d4straub commented Mar 28, 2024 •

edited

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github-actions bot commented Mar 28, 2024 •

edited

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

d4straub commented Apr 3, 2024 •

edited

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