2.0.0 Release #18

kylacochrane · 2024-04-18T19:56:41Z

Initial release of 2.0.0 for SpeciesAbundance as a nextflow pipleine.

Updating files associated with nf-core linting issues

Kraken Module Addition

Removed IridaNextExample modules/tests/data

* Adding the BRACKEN modules; updating modules/workflow to match; added python script for bracken * Formatting and troubleshooting * Update workflow; input taxonomic_level as Channel.value; remove .collect() * Removed print statements for debugging * Removed print statements for debugging * Fixed formatting with EC * Removed adjust_bracken.py file: meant for a different module * Updated files for GitHub testing of pipeline * Added mini kraken/bracken database for testing * Cleaned kmer_dist file in minidb * Added comment to bracken/main.nf

Adding the ADJUST_BRACKEN module and python code

Adding modules to pull the top_5 species kraken/bracken results and add the data in the correct format to the IRIDANext JSON file.

… by BRACKEN to estimate the abundance at a single taxonomic level

…files to come from a single shared directory. Updated nextflow.config, nextflow_schema.json, test.config, and main.nf.test to accomodate these changes

…Style-Report

…from ADJUST_BRACKEN and updated module requirements

…ad of percentages

Add additional functionality and final documentation for pipeline usage.

Updated versioning in CHANGELOG.md and nextflow.config

github-actions · 2024-04-18T19:57:51Z

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

Posted for pipeline commit f162cfe

+| ✅ 126 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.0.0
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

❔ 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 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-speciesabundance_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.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
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 Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
template_strings - Did not find any Jinja template strings (95 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: ci.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.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 '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 2024-04-19 13:11:06

apetkau

This is amazing work Kyla. I tested it all in Azure and it all works 😄 🥳

I do have one suggested change prior to releasing.

modules/local/kraken2/main.nf

apetkau

Looks amazing. Thanks so much 😄

kylacochrane added 30 commits March 12, 2024 16:53

Updating nf-core .github/workflows and .pre-commit-config.yaml files

94ca694

Fixing errors associated with nf-core lint

fad838e

Adjusted test.config max_memory

0b29aeb

Updated branch.yml to reference phac-nml

bfdd0c8

Merge pull request #4 from phac-nml/nf-core-linting

005ec05

Updating files associated with nf-core linting issues

Committing local changes before rebasing origin/dev

c580e2f

Fixed file formatting and linting

b9c476b

Adding the KRACKEN mini_gut database

be04c68

Changed db PATH to kraken branch to access minigut_kraken db

fbb000d

Updates for functionality of pipeline

172cee3

fixed EC whitespace in kraken2/main.nf

69a692d

Added when statement to kraken module

f8418f5

Set workflow variable meta.single_end and updated kraken module

7828098

Separated kraken module inputs so workflow can have separate channels

b639792

Separated output entries

5bb1238

Updated workflow kraken_db channel

d39bca1

Updated nextflow_schema.json

a2b375f

Updated kraken module to compress output txt and tsv files

3a76046

Formatting changes

b299e57

Merge pull request #5 from phac-nml/kraken

6d29fc9

Kraken Module Addition

Removed IridaNextExample modules/tests/data and inclusion in workflow

59f6bb5

Merge pull request #6 from phac-nml/remove_irida_modules

1f6d2d9

Removed IridaNextExample modules/tests/data

Adding the ADJUST_BRACKEN module and python script

3261690

Update README.md

a9028e5

Update README.md

081a614

Update README.md

46567b0

Updated python script comments

cab26de

Merge pull request #8 from phac-nml/adjustbracken

b00a361

Adding the ADJUST_BRACKEN module and python code

Added KRONA functionality

ea672bc

kylacochrane added 23 commits April 10, 2024 18:51

Updated function in bracken_top_n_linelist.py

cf88aae

Added comments to bracken_top_n_linelist.py

d6636da

Merge pull request #12 from phac-nml/top5

48ed2a1

Adding modules to pull the top_5 species kraken/bracken results and add the data in the correct format to the IRIDANext JSON file.

Updated module output nomenclature

fad7945

Update iridanext.config and main.nf.test

e27dbd5

Updated module naming for consistency (kraken2krona)

d009b7f

Added kmer_len as a parameter to set the kmer distribution files used…

6e75e48

… by BRACKEN to estimate the abundance at a single taxonomic level

Added additional workflow parameter to allow Kraken/Bracken database …

2c5431c

…files to come from a single shared directory. Updated nextflow.config, nextflow_schema.json, test.config, and main.nf.test to accomodate these changes

Formatting changes

eaaca57

Updated README.md

3c41163

Changed parameter name from 'combined_db' to 'database' for clarity

8e1d364

Updated output and usage documentation

66419b2

Updated main.nf.test database parameter

ec9de94

Update pyhton script in ADJUST_BRACKEN to output the Adjusted-Kraken-…

3a8113e

…Style-Report

Updated workflow [bracken2krona] to use Adjusted-Kraken-Style-Report …

b9ce5e9

…from ADJUST_BRACKEN and updated module requirements

Updated documentation

9439b86

Fixed main.nf.test

394e8bd

Added additional output tests

0c1a100

Update the adjust bracken abundances step to report proportions inste…

5071d42

…ad of percentages

Merge pull request #13 from phac-nml/add_docs

be3cfd8

Add additional functionality and final documentation for pipeline usage.

Updated versioning in CHANGELOG.md and nextflow.config

8a99747

Added link to Galaxy-based pipeline for reference

e3dbc5f

Merge pull request #17 from phac-nml/version

5ec0d15

Updated versioning in CHANGELOG.md and nextflow.config

kylacochrane marked this pull request as ready for review April 18, 2024 20:04

kylacochrane requested a review from apetkau April 18, 2024 20:04

apetkau requested changes Apr 18, 2024

View reviewed changes

modules/local/kraken2/main.nf Outdated Show resolved Hide resolved

Updated kraken2 process to high

f162cfe

apetkau approved these changes Apr 19, 2024

View reviewed changes

kylacochrane merged commit 8656f36 into main Apr 19, 2024
9 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

2.0.0 Release #18

2.0.0 Release #18

kylacochrane commented Apr 18, 2024

github-actions bot commented Apr 18, 2024 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

apetkau left a comment

apetkau left a comment

2.0.0 Release #18

2.0.0 Release #18

Conversation

kylacochrane commented Apr 18, 2024

github-actions bot commented Apr 18, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

apetkau left a comment

Choose a reason for hiding this comment

apetkau left a comment

Choose a reason for hiding this comment

github-actions bot commented Apr 18, 2024 •

edited

Loading

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