Readcov #193

DLBPointon · 2024-01-10T13:56:52Z

No description provided.

github-actions · 2024-01-10T13:58:55Z

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

Posted for pipeline commit 88f566f

+| ✅ 127 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: .github/workflows/awstest.yml
files_exist - File not found: .github/workflows/awsfulltest.yml
nextflow_config - Config manifest.version should end in dev: '1.0.2'
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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
system_exit - System.exit in WorkflowTreeval.groovy: System.exit(1) [line 17]

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-treeval_logo_light.png
files_exist - File is ignored: conf/test_full.config
files_exist - File is ignored: docs/images/nf-core-treeval_logo_light.png
files_exist - File is ignored: docs/images/nf-core-treeval_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/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-treeval_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_dark.png
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
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/treeval/treeval/.github/workflows/awstest.yml

✅ 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: 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: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: lib/WorkflowTreeval.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-treeval_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 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/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.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 - assets/email_template.txt matches the template
files_unchanged - docs/README.md 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
readme - README Nextflow minimum version badge matched config. Badge: 22.10.1, Config: 22.10.1
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (262 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/yaml'
schema_params - Schema matched params returned from nextflow config
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: sanger_test_full.yml
actions_schema_validation - Workflow validation passed: linting.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' 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 2.8
Run at 2024-01-11 18:25:48

DLBPointon

Just formatting suggestions

conf/modules.config

subworkflows/local/read_coverage.nf

assets/local_testing/nxOscDF5033.yaml

conf/modules.config

subworkflows/local/yaml_input.nf

DLBPointon · 2024-01-10T14:11:43Z

linting failing you need to run nf-core modules patch to fix

yumisims · 2024-01-10T14:13:04Z

Ok I will run and resubmit thanks From: Damon-Lee Pointon ***@***.***> Reply to: sanger-tol/treeval ***@***.***> Date: Wednesday, 10 January 2024 at 14:12 To: sanger-tol/treeval ***@***.***> Cc: Ying Sims ***@***.***>, Assign ***@***.***> Subject: Re: [sanger-tol/treeval] Readcov (PR #193) [EXT] linting failing you need to run nf-core modules patch to fix — Reply to this email directly, view it on GitHub [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_sanger-2Dtol_treeval_pull_193-23issuecomment-2D1884925168&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=X9VPYUGy4ibZarh9Rup1XaZ62i2u-I0xOZXEy11dXDM&m=Zf3BV4rrlwX-8B-At8EgG2q2joumnQmeRgBi0TUyRg8zYi9zyczGHsZUSpxSW0jk&s=dfpIplo6BuMexXCzD9FlVM72RRi4F0QPsc5WL4CEnT4&e=>, or unsubscribe [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ADHNWY5E3MSF4HITI4RJSVTYN2OSXAVCNFSM6AAAAABBU2XD6CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBUHEZDKMJWHA&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=X9VPYUGy4ibZarh9Rup1XaZ62i2u-I0xOZXEy11dXDM&m=Zf3BV4rrlwX-8B-At8EgG2q2joumnQmeRgBi0TUyRg8zYi9zyczGHsZUSpxSW0jk&s=KSrJCiSzG71nHYBtmplLO-gAeFmxfAMl1IO_mkpSOyA&e=>. You are receiving this because you were assigned.Message ID: ***@***.***>

…

-- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA

yumisims added 6 commits December 18, 2023 21:12

add read_coverage, se_mapping and pe_mapping

0666c5b

read coverage completed

9e3627a

change config

64b6f75

changed byte size

b2773e8

changed minimap2 module

9dbd91e

changed format

34db5ae

DLBPointon added this to the Release 1 milestone Jan 10, 2024

DLBPointon requested a review from weaglesBio January 10, 2024 13:56

DLBPointon assigned yumisims Jan 10, 2024

DLBPointon commented Jan 10, 2024

View reviewed changes

weaglesBio requested changes Jan 10, 2024

View reviewed changes

assets/local_testing/nxOscDF5033.yaml Outdated Show resolved Hide resolved

conf/modules.config Show resolved Hide resolved

subworkflows/local/yaml_input.nf Outdated Show resolved Hide resolved

yumisims added 11 commits January 10, 2024 14:17

patch fix

e5c1e95

changes based on comments

afc9cd7

add channel from galaxy

e0b24e9

Merge branch 'galaxy_dev' into readcov

6e859ed

removed longread_coverage from rapid

9011845

corrected workflow name

b83b0b9

changed reads_ch to read_ch

f0e8f84

changed reads_ch to read_ch

d531930

changed reads_ch to read_ch

606c606

changed reads_ch to read_ch

06c0454

changed reads_ch to read_ch

88f566f

DLBPointon merged commit 6af7247 into galaxy_dev Jan 12, 2024
6 checks passed

DLBPointon deleted the readcov branch January 12, 2024 10:03

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Readcov #193

Readcov #193

DLBPointon commented Jan 10, 2024

github-actions bot commented Jan 10, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

DLBPointon left a comment

DLBPointon commented Jan 10, 2024

yumisims commented Jan 10, 2024 via email

Readcov #193

Readcov #193

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DLBPointon commented Jan 10, 2024

github-actions bot commented Jan 10, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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DLBPointon commented Jan 10, 2024

yumisims commented Jan 10, 2024 via email

github-actions bot commented Jan 10, 2024 •

edited

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