Updating everything #17

DLBPointon · 2024-02-06T16:14:07Z

Updating the map generation workflows and adding pretext ingestion

github-actions · 2024-02-06T16:16:00Z

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

Posted for pipeline commit 9d9f779

+| ✅ 130 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in base.config: Check the defaults for all processes
schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: assets/nf-core-curationpretext_logo_light.png
files_exist - File is ignored: docs/images/nf-core-curationpretext_logo_light.png
files_exist - File is ignored: docs/images/nf-core-curationpretext_logo_dark.png
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: .github/workflows/linting.yml
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-curationpretext_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-curationpretext_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-curationpretext_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
multiqc_config - 'assets/multiqc_config.yml' not found

✅ 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: 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: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreSchema.groovy
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: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowCurationpretext.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: .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-curationpretext_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.show_hidden_params
nextflow_config - Config variable found: params.schema_ignore_params
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 manifest.version ends in dev: '1.0dev'
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
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 - assets/email_template.html matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreSchema.groovy matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 22.10.1, Config: 22.10.1
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (206 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: sanger_test.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: sanger_test_full.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
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.8
Run at 2024-07-05 09:29:59

Updating all modules

… being used

…files

DLBPointon · 2024-07-04T18:55:09Z

Can you check the final software_versions.yml to make sure all versions are filled in ?

Can confirm, that the software_versions.yml is being generated and filled in.

docs/usage.md

DLBPointon · 2024-07-05T08:57:25Z

Pipeline now passes CICD

Updating everything

cadd40c

DLBPointon added the enhancement New feature or request label Feb 6, 2024

DLBPointon self-assigned this Feb 6, 2024

DLBPointon and others added 26 commits February 6, 2024 16:20

Updating testing

389caeb

Forgotten module

bad5076

Channel assignment

73cbd14

Messed up workflow

27e1a3f

Messed up workflow

98d36ef

Messed up workflow

644b0b1

Messed up workflow

c59909c

Getting closer to parity with TreeVal

d2144be

Resource corrections

c254312

Resource corrections

8b7e2be

Missing files and incorrect arg

8994796

Linting and removed docker.useremulation

a3c792e

Ci fix

e089acd

Ci fix

9ea01a4

Ci fix

fd4f5bd

Updating all modules

4da9378

Linting

9b09fa7

Variable misspell

8f17dbf

Updating the pretext modules to use local pretext software

0360796

Merge pull request #18 from sanger-tol/dp24_modules_update

9e0eca6

Updating all modules

updating documents also caught bug that was stopping params file from…

1c23e8b

… being used

Merge branch 'dp24_treeval_parity' into dp24_docs_update

7ecef09

caught a rogue pacbio!

2045e35

prettier

b5814ae

subworkflow updates

226b4dd

subworkflow updates

5c4c467

DLBPointon added 11 commits May 24, 2024 10:29

Fixed error where I had created a malformed channel inside a channel

145db15

Update for linting

ad1f4d6

Erroneous '''

c69ea4c

Erroneous '''

43f7b1e

Update to Lisence for Arima Script

b00bb0f

Updating test data and temp dir in modules

d65efb8

Fixed the RIGHT files for the test data

35e87e8

Fixed the pattern for input

ac9e5f4

Comment out two lines which check file location, doesn't work for s3 …

a3fe905

…files

Comment out two lines which check file location, doesn't work for s3 …

d36ecb5

…files

Reverting change to tests and param checks

ff56482

DLBPointon requested a review from muffato May 24, 2024 15:52

DLBPointon added 3 commits May 28, 2024 13:09

Update minimap2 align algorithm

c521a87

Logo for the pipeline

f44a52b

Adding the new logo for the pipeline, only in light version

9b11919

DLBPointon added 3 commits July 4, 2024 19:55

2nd Parity update to 1.1.1 treeval

5e22cd9

Update to linting

2e26ea7

linting

2f0fd0d

muffato reviewed Jul 4, 2024

View reviewed changes

docs/usage.md Outdated Show resolved Hide resolved

DLBPointon added 2 commits July 5, 2024 09:22

Update to download containers before running pipeline

419ca9b

Update to download containers before running pipeline

a07757e

Update version in command

01c23d1

DLBPointon requested a review from muffato July 5, 2024 08:58

DLBPointon added 2 commits July 5, 2024 10:14

DARK MODE!

fbea6a4

Update for Dark mode

9d9f779

muffato approved these changes Jul 5, 2024

View reviewed changes

DLBPointon merged commit c0650ec into dev Jul 8, 2024
6 checks passed

DLBPointon deleted the dp24_treeval_parity branch July 8, 2024 08:48

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Updating everything #17

Updating everything #17

DLBPointon commented Feb 6, 2024

github-actions bot commented Feb 6, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

DLBPointon commented Jul 4, 2024

DLBPointon commented Jul 5, 2024

Updating everything #17

Updating everything #17

Conversation

DLBPointon commented Feb 6, 2024

github-actions bot commented Feb 6, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

DLBPointon commented Jul 4, 2024

DLBPointon commented Jul 5, 2024

github-actions bot commented Feb 6, 2024 •

edited

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