Update to version 0.3.0 #30

kylacochrane · 2024-09-05T14:41:44Z

Update gasclustering to version 0.3.0.

See CHANGELOG.md for updates.

…port format

… Locidex mlst.json report format

…rom ci.yml and add to modules.conf

…assure.py

Update/input assure to accommodate changes in locidex mlst.json allele reports

github-actions · 2024-09-05T14:43:06Z

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

Posted for pipeline commit 0c35862

+| ✅ 147 tests passed       |+
#| ❔  27 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 0.3.0
schema_lint - Schema $id should be https://raw.githubusercontent.com/phac-nml/gasclustering/master/nextflow_schema.json
Found https://raw.githubusercontent.com/phac-nml/gasclustering/main/nextflow_schema.json

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-gasclustering_logo_light.png
files_exist - File is ignored: docs/images/nf-core-gasclustering_logo_light.png
files_exist - File is ignored: docs/images/nf-core-gasclustering_logo_dark.png
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: lib/Utils.groovy
files_exist - File is ignored: lib/WorkflowMain.groovy
files_exist - File is ignored: lib/NfcoreTemplate.groovy
files_exist - File is ignored: lib/WorkflowGasclustering.groovy
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
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/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-gasclustering_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-gasclustering_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-gasclustering_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/gasclustering/gasclustering/.github/workflows/awstest.yml
actions_awsfulltest - actions_awsfulltest
pipeline_name_conventions - pipeline_name_conventions

✅ 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: 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: 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: modules.json
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: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
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: docs/images/nf-core-gasclustering_logo.png
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: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
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.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 - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.metadata_1_header= metadata_1
nextflow_config - Config default value correct: params.metadata_2_header= metadata_2
nextflow_config - Config default value correct: params.metadata_3_header= metadata_3
nextflow_config - Config default value correct: params.metadata_4_header= metadata_4
nextflow_config - Config default value correct: params.metadata_5_header= metadata_5
nextflow_config - Config default value correct: params.metadata_6_header= metadata_6
nextflow_config - Config default value correct: params.metadata_7_header= metadata_7
nextflow_config - Config default value correct: params.metadata_8_header= metadata_8
nextflow_config - Config default value correct: params.pd_outfmt= matrix
nextflow_config - Config default value correct: params.pd_distm= hamming
nextflow_config - Config default value correct: params.pd_missing_threshold= 1.0
nextflow_config - Config default value correct: params.pd_sample_quality_threshold= 1.0
nextflow_config - Config default value correct: params.pd_file_type= text
nextflow_config - Config default value correct: params.gm_thresholds= 10,5,0
nextflow_config - Config default value correct: params.gm_method= average
nextflow_config - Config default value correct: params.gm_delimiter= .
nextflow_config - Config default value correct: params.max_cpus= 4
nextflow_config - Config default value correct: params.max_memory= 2.GB
nextflow_config - Config default value correct: params.max_time= 1.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.validate_params= true
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml 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 Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
template_strings - Did not find any Jinja template strings (151 files)
schema_lint - Schema 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: branch.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.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 found and not ignored.
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'
base_config - conf/base.config found and not ignored.
base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - INPUT_ASSURE found in conf/modules.config and Nextflow scripts.
modules_config - GAS_MCLUSTER found in conf/modules.config and Nextflow scripts.
modules_config - LOCIDEX_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - PROFILE_DISTS found in conf/modules.config and Nextflow scripts.
modules_config - ARBOR_VIEW found in conf/modules.config and Nextflow scripts.
modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-09-10 15:51:51

apetkau

Looks good. One small change 😄

assets/samplesheet.csv

apetkau

Thanks so much.

apetkau

Looks great to me. Thanks so much Kyla 😄

kylacochrane added 23 commits August 15, 2024 14:50

Update locidex container registry

09efa91

Update input_assure.py to accomodate the revised Locidex mlst.json re…

9e820c8

…port format

Update test data (reports and samplesheets) to accomodate the revised…

29debe1

… Locidex mlst.json report format

Update paths to mlst files in samplesheet.csv

2cb4888

Fixed error in samplesheet

cc1444b

Fixed typo

9a87a2b

Updated container registry handling

307aa82

add user UID/GID to Nextflow Docker run in CI to fix getpwuid() error

29d427f

add root user to Nextflow Docker run in CI to fix getpwuid() error

09cfa2b

Updated container for arborview

2639645

Refactor user configuration for locidex module: Remove --user specs f…

726d2c9

…rom ci.yml and add to modules.conf

Revert to previous user config in ci.yml

8a016b4

Update --user in ci.yml

eac46d8

Removed --user configurations for locidex

db503bf

Updated CHANGELOG.md

1aebb70

Updated release version

f3f83cd

Removed print debugging statement in input_assure.py

a23379c

Replace unsorted list with sorted() for consistent ordering in input_…

6f7f59d

…assure.py

Update locidex to version 0.2.3

f787028

Add link to release tag

cf5248e

Merge pull request #28 from phac-nml/update/input_assure

1042780

Update/input assure to accommodate changes in locidex mlst.json allele reports

Update CHANGELOG

e653503

Update test data file paths in samplesheets

dc32ebb

kylacochrane marked this pull request as ready for review September 5, 2024 15:07

kylacochrane requested review from emarinier and apetkau September 5, 2024 15:07

emarinier approved these changes Sep 5, 2024

View reviewed changes

apetkau requested changes Sep 5, 2024

View reviewed changes

assets/samplesheet.csv Outdated Show resolved Hide resolved

update assest/samplesheet.csv file paths

b60e1d3

apetkau approved these changes Sep 5, 2024

View reviewed changes

kylacochrane added 2 commits September 10, 2024 11:46

Update profile_dist container

0071ab8

Update CHANGELOG

0c35862

apetkau approved these changes Sep 10, 2024

View reviewed changes

kylacochrane merged commit 9bbd787 into main Sep 10, 2024
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Update to version 0.3.0 #30

Update to version 0.3.0 #30

kylacochrane commented Sep 5, 2024

github-actions bot commented Sep 5, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

apetkau left a comment

apetkau left a comment

apetkau left a comment

Update to version 0.3.0 #30

Update to version 0.3.0 #30

Conversation

kylacochrane commented Sep 5, 2024

github-actions bot commented Sep 5, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

apetkau left a comment

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github-actions bot commented Sep 5, 2024 •

edited

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