Release 0.2.0 #87

priyanka-surana · 2023-12-22T09:45:46Z

This is a quick release. No reviews are being done.

Merging main into dev

setting for v0.2.0

change uniprot database names Co-authored-by: Priyanka Surana <[email protected]>

Co-authored-by: Priyanka Surana <[email protected]>

Prod release v0.2.0 - proper review not done

github-actions · 2023-12-22T09:47:20Z

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

Posted for pipeline commit bc9fa62

+| ✅ 135 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 0.2.0

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/nf-core-blobtoolkit_logo_light.png
files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_light.png
files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_dark.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: conf/igenomes.config
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/nf-core-blobtoolkit_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/blobtoolkit/blobtoolkit/.github/workflows/awstest.yml
template_strings - template_strings
merge_markers - merge_markers

✅ 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: 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/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: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
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/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: lib/WorkflowBlobtoolkit.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-blobtoolkit_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: .travis.yml
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: 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 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
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml 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 - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar 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
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
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: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: sanger_test_full.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: sanger_test.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: ci.yml
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 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.11.1
Run at 2023-12-22 09:47:01

priyanka-surana and others added 30 commits May 18, 2023 22:02

Merge pull request #72 from sanger-tol/main

c5e1cea

Merging main into dev

nextflow version update

192ad74

pipeline version update

445b9e7

setup CHANGELOG for next version

a2bab9b

prettier fix

fa33c9a

Merge pull request #73 from sanger-tol/new_version

db7c9e1

setting for v0.2.0

added chunk_busco module

b2e2e06

added diamond_blastx module

a833404

added blastx_cols and blastx_outext

94b44c9

fix DIAMOND_BLASTX path

46ae681

added module BLOBTOOLKIT_UNCHUNK

b5594c4

diamond_blastx data for test_full

4c3e944

removed log files

40c212a

fix path to uniprot_blastx

0ae6480

renamed files in RUN_BLASTX subworkflow

a7502f0

use meta and meta2

8de106a

use names in RUN_BLASTX input channels

5466144

added uniprot_blastx

d667473

merge blastx results in BlobDir

49cb8bf

minimum Nextflow version 23.04.1

abc2b97

update uniprot databases

7bd7873

updated paths to uniprot databases

cec0022

Introduced the basal lineages as a configurable parameter

5011a18

Update conf/test.config

ddb9645

change uniprot database names Co-authored-by: Priyanka Surana <[email protected]>

use new names for uniprot databases

d814e5f

Update modules/local/blobtoolkit/chunk.nf

3bc14aa

Co-authored-by: Priyanka Surana <[email protected]>

update names for uniprot databases

72f040c

fix description

0dbc9b6

update uniprot database names

c8bef6c

check params.blastp and params.blastx

1c9f9c4

priyanka-surana and others added 26 commits December 18, 2023 23:03

get the pipeline working

da3b983

prettier fix

9107ed6

adding missing data

3836eda

working version

dad639a

linting fix

387b6b6

Template update for nf-core/tools version 2.11

8ad250a

nf-core v2.11 update

458d0ce

Remove fastqc

3716907

prettier fix

464660b

fix params location

d175795

add missing comma

7e1774e

updating busco database

949a947

update docker runOptions

16d200d

Template update for nf-core/tools version 2.11.1

7849589

Merge branch 'TEMPLATE' into blast

8e8c1a9

update btk version

8ef790d

update blobtk naming

45639a7

update CHANGELOG

4cbf587

update citations

995d8b0

update README

b712e30

update docs

2b8dc5b

nf-core lint release fix

e0987f9

working version

da8632c

black fix

c45daa9

push busco results

f0a74af

Merge pull request #85 from sanger-tol/blast

bc9fa62

Prod release v0.2.0 - proper review not done

priyanka-surana changed the title ~~Dev~~ Release 0.2.0 Dec 22, 2023

priyanka-surana requested a review from alxndrdiaz December 22, 2023 09:58

priyanka-surana merged commit 735b30d into main Dec 22, 2023
12 checks passed

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Release 0.2.0 #87

Release 0.2.0 #87

priyanka-surana commented Dec 22, 2023

github-actions bot commented Dec 22, 2023 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Release 0.2.0 #87

Release 0.2.0 #87

Conversation

priyanka-surana commented Dec 22, 2023

github-actions bot commented Dec 22, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

github-actions bot commented Dec 22, 2023 •

edited

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