Release 0.1.0 #6

sgsutcliffe · 2024-12-13T19:03:31Z

0.1.0 - 2024-12-13

Release

fastmatchirida is built using gasclustering 0.4.0 as a template. The goal of the release is to set up the basic-functionality of the pipeline for testing in IRIDA-Next.

Pipeline Description

The pipline will be used, integrated into IRIDA-Next, to allow users to select reference samples that meet with a minimum threshold distance to a query set of samples for downstream analysis. The output is a table (tsv and excel) of the samples that match the minium threshold distance.

De gasclustering pipeline

…IDIA

Result Retrieval from FastMatch Pipeline

Input Data to the FastMatch Pipeline

Define Query & Reference Samples

Adds Program Outputs to Irida Next JSON Output File

github-actions · 2024-12-13T19:05:00Z

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

Posted for pipeline commit 9c5f0ef

+| ✅ 143 tests passed       |+
#| ❔  28 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes_ignored.config
nextflow_config - nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/
nextflow_config - Config manifest.version should end in dev: 0.1.0
schema_lint - Schema $id should be https://raw.githubusercontent.com/phac-nml/fastmatchirida/master/nextflow_schema.json
Found https://raw.githubusercontent.com/phac-nml/fastmatchirida/main/nextflow_schema.json

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-fastmatchirida_logo_light.png
files_exist - File is ignored: docs/images/nf-core-fastmatchirida_logo_light.png
files_exist - File is ignored: docs/images/nf-core-fastmatchirida_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/Workflowfastmatchirida.groovy
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
nextflow_config - Config variable ignored: params.max_cpus
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-fastmatchirida_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-fastmatchirida_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-fastmatchirida_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/fastmatchirida/fastmatchirida/.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-fastmatchirida_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: lib/WorkflowFastmatchirida.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 - Found nf-validation plugin
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: 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.threshold= 1.0
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.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
plugin_includes - No wrong validation plugin imports have been found
template_strings - Did not find any Jinja template strings (0 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: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.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 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 - LOCIDEX_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - PROFILE_DISTS 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: 3.0.1

Run details

nf-core/tools version 3.0.1
Run at 2024-12-13 19:07:46

sgsutcliffe and others added 30 commits December 9, 2024 15:09

Renaming files from gasclustering to fastmatchirida

3a3289f

Removed everything after profile_dist

346a9c5

Fix Nextflow-Setup Issue with CI

82954b2

Fix lint issue with removed modules

ff3f028

Merge pull request #1 from phac-nml/de-gasclustering-pipeline

cbea074

De gasclustering pipeline

Limit iridanext output to fastmatch files

346311e

First attempt to modify IRIDA UI

1efe47c

Modified the UI to include query reference

aa4e0bd

Forgot to check prettier

dc91ff4

Modification to UI

6448399

Very basic output framework.

4448ac1

pairwise output format, appending metadata

d579c35

Cleaning up, process_output.py outputs the input for now.

6ee6358

Convert blank column entries of fastmatch_category to reference

b12fb5c

Make reference the default if left blank and fix drop down menu in IR…

fa831f7

…IDIA

Both sample names and sample/Irida IDs in output.

2f08dd1

Distance threshold.

2121cfd

Removing profile dist output format from schema.

4a2138c

threshold as a parameter

34b8373

Newline at end of file.

eb173c2

Updated script example.

8ade704

Updating container

75013de

Set minimum for threshold to 0

8de39dd

Updating test data after switching to pairwise output.

0699fca

Check scaled values in range between 0-100

a70d030

xlsx, float threshold

4c18be3

Merge pull request #3 from phac-nml/output-stub

70962d5

Result Retrieval from FastMatch Pipeline

Merge pull request #2 from phac-nml/input-interface

25f22dd

Input Data to the FastMatch Pipeline

Seperated reference and query for profile dist

f1c2fc6

Remove gm_threshold tests (GAS Cluster)

c0ebde3

emarinier and others added 8 commits December 13, 2024 09:29

Updating Irida Next JSON outputs.

d0c751c

Updating tests.

6b3fa13

Add query set to reference set

cf6685c

Reduced tests to simply workflow.success for now

c82c6f9

Merge pull request #4 from phac-nml/define-queryref

484c1b6

Define Query & Reference Samples

Merge pull request #5 from phac-nml/update-json

8c43747

Adds Program Outputs to Irida Next JSON Output File

Updated release date

916dfa2

Updated release date

d8a7c31

Remove index on excel output

9c5f0ef

sgsutcliffe merged commit 5060b49 into main Dec 13, 2024
9 checks passed

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Release 0.1.0 #6

Release 0.1.0 #6

sgsutcliffe commented Dec 13, 2024

github-actions bot commented Dec 13, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Release 0.1.0 #6

Release 0.1.0 #6

Conversation

sgsutcliffe commented Dec 13, 2024

0.1.0 - 2024-12-13

Release

Pipeline Description

github-actions bot commented Dec 13, 2024 • edited Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

github-actions bot commented Dec 13, 2024 •

edited

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