Update to Version 2.1.0 #25

kylacochrane · 2024-09-26T16:04:30Z

Update speciesabundance to version 2.2.0.

See CHANGELOG.md for updates.

…column based on 'sample' (meta.irida_id) for proper nf-iridanext plugin metadata functionality.

…s not provided in the samplesheet

…ted in the input samplesheet.

Enhanced pipeline logic to support user-defined `sample_name` input

github-actions · 2024-09-26T16:05:49Z

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

Posted for pipeline commit a190410

+| ✅ 134 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.2.0
schema_lint - Schema $id should be https://raw.githubusercontent.com/phac-nml/speciesabundance/master/nextflow_schema.json
Found https://raw.githubusercontent.com/phac-nml/speciesabundance/main/nextflow_schema.json
nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-speciesabundance_logo_light.png
files_exist - File is ignored: docs/images/nf-core-speciesabundance_logo_light.png
files_exist - File is ignored: docs/images/nf-core-speciesabundance_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/WorkflowSpeciesabundance.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-speciesabundance_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-speciesabundance_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-speciesabundance_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/speciesabundance/speciesabundance/.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-speciesabundance_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.taxonomic_level= S
nextflow_config - Config default value correct: params.kmer_len= 100
nextflow_config - Config default value correct: params.top_n= 5
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
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore 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 (106 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: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.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 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 - SAMPLESHEET_CHECK found in conf/modules.config and Nextflow scripts.
modules_config - FASTP_TRIM found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN2 found in conf/modules.config and Nextflow scripts.
modules_config - BRACKEN 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

Run details

nf-core/tools version 2.14.1
Run at 2024-09-26 16:05:29

apetkau

Looks great. Thanks so much 😄

kylacochrane added 17 commits August 7, 2024 14:59

Enhanced pipeline logic to support user-defined

d3e2792

Updated processes to ensure CSVTK generates files with a 'sample_id' …

25984f7

…column based on 'sample' (meta.irida_id) for proper nf-iridanext plugin metadata functionality.

Fixed liniting and EC issues

822e93d

Updated CI testing to incorporate sample_name.

03933e8

Update workflow logic to et meta.id to meta.irida_if if sample_name i…

e4a1ae0

…s not provided in the samplesheet

Enhanced test coverage by adding a scenario where sample_name is omit…

94bc34c

…ted in the input samplesheet.

Fixed linting issue

b96f2bc

Fixed typo

3a081bb

Replace non-alphanumeric characters in sample IDs with underscores

cc6a23d

Updated main.nf.test to include tests for various sample_name scenarios

5dd474e

Update input_schema

f56b9e7

Update documentation

4a457d9

Updated README.md

b78388a

Updates to documentation for readability

1af1a8f

Edits to README and usage docs

f6e6b0f

Merge pull request #24 from phac-nml/add_sample_name

513b58b

Enhanced pipeline logic to support user-defined `sample_name` input

Updated versioning in CHANGELOG and nextflow.config

a190410

kylacochrane marked this pull request as ready for review September 26, 2024 16:42

kylacochrane requested a review from apetkau September 26, 2024 16:42

apetkau approved these changes Sep 26, 2024

View reviewed changes

kylacochrane merged commit f0a639d into main Sep 26, 2024
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Update to Version 2.1.0 #25

Update to Version 2.1.0 #25

kylacochrane commented Sep 26, 2024

github-actions bot commented Sep 26, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

apetkau left a comment

Update to Version 2.1.0 #25

Update to Version 2.1.0 #25

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kylacochrane commented Sep 26, 2024

github-actions bot commented Sep 26, 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 26, 2024 •

edited

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