Update modules and fix bugs for v2.5 release #314

drpatelh · 2022-07-07T15:01:31Z

Updated

Bumped tool versions in Bump tool versions for modules required in viralrecon modules#1859 and re-installed in the pipeline
Bump pipeline version to 2.5

Fixed

[#234] - Remove replacement of dashes in sample name with underscores
[#292] - Filter empty FastQ files after adapter trimming
[#303] - New pangolin dbs (4.0.x) not assigning lineages to Sars-CoV-2 samples in MultiQC report correctly
[#306] - Add contig field information in vcf header in ivar_variants_to_vcf and use bcftools sort
[#311] - Invalid declaration val medaka_model_string

github-actions · 2022-07-07T15:03:34Z

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

Posted for pipeline commit 96c5d3e

+| ✅ 138 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '2.5'
readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: lib/WorkflowViralrecon.groovy
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: lib/NfcoreTemplate.groovy
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: .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: assets/nf-core-viralrecon_logo_light.png
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/images/nf-core-viralrecon_logo_light.png
files_exist - File found: docs/images/nf-core-viralrecon_logo_dark.png
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: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
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-viralrecon_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
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: manifest.homePage
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.version
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 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 manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
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 - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.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 - .github/workflows/linting.yml matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-viralrecon_logo_light.png matches the template
files_unchanged - docs/images/nf-core-viralrecon_logo_light.png matches the template
files_unchanged - docs/images/nf-core-viralrecon_logo_dark.png 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
files_unchanged - .gitignore 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 in Quick Start section matched config. README: 21.10.3, Config: 21.10.3
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (245 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.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

Run details

nf-core/tools version 2.4.1
Run at 2022-07-12 10:50:12

drpatelh added 5 commits July 7, 2022 11:23

Follow up fix for PR nf-core#308

2919d30

Run nf-core modules update

5c07e17

Intentionally ignore expected nf-core warnings

8049c25

Re-install nf-core modules after updating tool versions

f106faf

Re-install nf-core modules after updating tool versions

7561671

drpatelh mentioned this pull request Jul 7, 2022

update conda recipe for artic minion #313

Closed

10 tasks

drpatelh added 17 commits July 8, 2022 17:16

Fix tests after updating tool versions for all modules

f770367

Revert version bumps for SnpEff and SnpSift

92a0ce3

Fix incorrect container definitions for SnpEff and SnpSift

734a4da

Fix ECLint

f2c5adf

Fix nf-core#292

a1f810b

Fix nf-core#292 again

6a0bc31

Fix config bug - see issue 1722 on MultiQC repo

af9cfe8

Add print statement back into ivar_variants_to_vcf.py scrip

95c0cc2

Fix Pangolin and Nextclade lineage parsing issues

7464f88

Fix publishDir bug introduced in PR 308

678e235

Fix nf-core#311

cb7efb7

Fix nf-core#234

81e03d5

Bump pipeline version to 2.5

ab88946

Fix publishing config relative to v2.4.1

cf4e8df

Update CHANGELOG

62b73dc

Add manual version definition for artic modules

1a8a3c0

Update docs to update default Nextclade version being used

96c5d3e

svarona approved these changes Jul 12, 2022

View reviewed changes

drpatelh changed the title ~~Update local and nf-core/modules in the pipeline~~ Update modules and fix bugs for v2.5 release Jul 12, 2022

drpatelh merged commit 429a5ff into nf-core:dev Jul 12, 2022

drpatelh mentioned this pull request Jul 12, 2022

Dev -> Master for 2.5 release #315

Merged

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Update modules and fix bugs for v2.5 release #314

Update modules and fix bugs for v2.5 release #314

drpatelh commented Jul 7, 2022 •

edited

github-actions bot commented Jul 7, 2022 •

edited

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Update modules and fix bugs for v2.5 release #314

Update modules and fix bugs for v2.5 release #314

Conversation

drpatelh commented Jul 7, 2022 • edited

Updated

Fixed

github-actions bot commented Jul 7, 2022 • edited

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

drpatelh commented Jul 7, 2022 •

edited

github-actions bot commented Jul 7, 2022 •

edited

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