Patch release: 1.1.5 #443

sofstam · 2024-02-01T13:44:33Z

Patch release: 1.1.5

PR checklist

Bump pipeline 1.1.4 version into dev

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Include a pre-built kaiju indexes in tutorial.md

Adding shortread deduplication feature with fastp

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Template update for nf-core/tools v2.12

github-actions · 2024-02-01T13:49:04Z

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

Posted for pipeline commit 8018d50

+| ✅ 194 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.1.5

✅ 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-taxprofiler_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-taxprofiler_logo_light.png
files_exist - File found: docs/images/nf-core-taxprofiler_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/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.yml
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/WorkflowTaxprofiler.groovy
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-taxprofiler_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/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://github.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.preprocessing_qc_tool= fastqc
nextflow_config - Config default value correct: params.shortread_qc_tool= fastp
nextflow_config - Config default value correct: params.shortread_qc_minlength= 15
nextflow_config - Config default value correct: params.shortread_complexityfilter_tool= bbduk
nextflow_config - Config default value correct: params.shortread_complexityfilter_entropy= 0.3
nextflow_config - Config default value correct: params.shortread_complexityfilter_bbduk_windowsize= 50
nextflow_config - Config default value correct: params.shortread_complexityfilter_fastp_threshold= 30
nextflow_config - Config default value correct: params.shortread_complexityfilter_prinseqplusplus_mode= entropy
nextflow_config - Config default value correct: params.shortread_complexityfilter_prinseqplusplus_dustscore= 0.5
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_minlength= 1000
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_keeppercent= 90
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_targetbases= 500000000
nextflow_config - Config default value correct: params.diamond_output_format= tsv
nextflow_config - Config default value correct: params.kaiju_taxon_rank= species
nextflow_config - Config default value correct: params.krakenuniq_ram_chunk_size= 16G
nextflow_config - Config default value correct: params.krakenuniq_batch_size= 20
nextflow_config - Config default value correct: params.malt_mode= BlastN
nextflow_config - Config default value correct: params.kmcp_mode= 3
nextflow_config - Config default value correct: params.ganon_report_type= reads
nextflow_config - Config default value correct: params.ganon_report_toppercentile= 0
nextflow_config - Config default value correct: params.ganon_report_mincount= 0
nextflow_config - Config default value correct: params.ganon_report_maxcount= 0
nextflow_config - Config default value correct: params.standardisation_taxpasta_format= tsv
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://github.com/nf-core/configs/master
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.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.igenomes_base= s3://ngi-igenomes/igenomes/
files_unchanged - .gitattributes matches the template
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-taxprofiler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-taxprofiler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-taxprofiler_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/NfcoreTemplate.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml 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: 23.04.0, Config: 23.04.0
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 (250 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: release-announcements.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
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: awsfulltest.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 2.12.1
Run at 2024-02-08 09:51:16

Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>

Centrifuge update to address mkfifo clashes

jfy133 · 2024-02-06T08:54:33Z

@sofstam could you make a PR into dev with a version bump?

sofstam · 2024-02-06T08:55:16Z

Yes, I can do that!

Bump version

LilyAnderssonLee

Well done!

CHANGELOG.md

docs/usage/tutorials.md

Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>

nf-core-bot and others added 29 commits January 25, 2024 10:23

Bump 1.1.4 version into dev

0df7715

Correct version

35c2482

Correct version

ba558e8

Correct v1.1.5dev

c263ea8

Merge pull request #436 from genomic-medicine-sweden/bump_release_1.1.4

53d191a

Bump pipeline 1.1.4 version into dev

add fastp dedup

6c752a9

Merge branch 'fastp_dedup' into dev

837a239

update changelog

2570c0f

Update CHANGELOG.md

e6fdf57

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update nextflow_schema.json

6867467

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update nextflow_schema.json

47edb12

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Include a pre-built kaiju indexes in tutorial.md

6192222

update changelog.md

1e1c9aa

Merge pull request #440 from nf-core/kaiju-prebuilt-indexes

0e1d46e

Include a pre-built kaiju indexes in tutorial.md

Merge branch 'dev' into dedup

1fed057

Prettier

ea35f93

Template update for nf-core/tools version 2.12

3df734d

Merge branch 'dev' into nf-core-template-merge-2.12

821a933

Fix trailing whitespace

b1250ac

Amount of left-padding spaces

0411f75

Left-padding spaces and trailing whitespace

080c094

Apply suggestions from code review

7e3f119

Merge pull request #439 from maxibor/dedup

0792d91

Adding shortread deduplication feature with fastp

Fix linting

1365e18

Prettier

dba2be8

Prettier

0f04072

Update README.md

568860a

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update nextflow.config

cdc36f1

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Merge pull request #442 from nf-core/nf-core-template-merge-2.12

98ddd10

Template update for nf-core/tools v2.12

sofstam closed this Feb 1, 2024

sofstam reopened this Feb 1, 2024

jfy133 and others added 7 commits February 3, 2024 14:50

Bump centrifuge version to hopefully fix mkfifo errors

f277760

Update CHANGELOG

6b255de

More Changelog updates

ba5c7c1

Apply suggestions from code review

de2a4fa

Update CHANGELOG.md

003bad1

Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>

Kreport friendly container

f9aee61

Merge pull request #444 from nf-core/centrifuge-update

1e414ef

Centrifuge update to address mkfifo clashes

jfy133 marked this pull request as ready for review February 6, 2024 08:54

jfy133 changed the title ~~Dev~~ Patch release: 1.1.5 Feb 6, 2024

sofstam and others added 3 commits February 8, 2024 09:36

Bump version

77c0ccb

Update CHANGELOG.md

9b5dd37

Merge pull request #445 from genomic-medicine-sweden/dev

ba126d8

Bump version

sofstam requested review from jfy133 and a team February 8, 2024 09:12

LilyAnderssonLee approved these changes Feb 8, 2024

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jfy133 and others added 2 commits February 8, 2024 10:48

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Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>

Apply suggestions from code review

8018d50

Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>

jfy133 approved these changes Feb 8, 2024

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sofstam merged commit 9f47401 into master Feb 8, 2024
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Patch release: 1.1.5 #443

Patch release: 1.1.5 #443

sofstam commented Feb 1, 2024 •

edited

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github-actions bot commented Feb 1, 2024 •

edited

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❗ Test warnings:

✅ Tests passed:

Run details

jfy133 commented Feb 6, 2024

sofstam commented Feb 6, 2024

LilyAnderssonLee left a comment

Patch release: 1.1.5 #443

Patch release: 1.1.5 #443

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sofstam commented Feb 1, 2024 • edited Loading

PR checklist

github-actions bot commented Feb 1, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

jfy133 commented Feb 6, 2024

sofstam commented Feb 6, 2024

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sofstam commented Feb 1, 2024 •

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github-actions bot commented Feb 1, 2024 •

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