Dev -> Master for 2.5 release #315

drpatelh · 2022-07-12T12:17:10Z

Changes listed here:
#314 (comment)

Bump pipeline version to 2.5dev

Update CHANGELOG after merging template updates

Re-factor code (proposal) for ivar_variants_to_vcf script

Update modules and fix bugs for v2.5 release

github-actions · 2022-07-12T12:19:08Z

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

Posted for pipeline commit 74ee2b6

+| ✅ 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 2022-07-13 14:09:51

JoseEspinosa

LGTM Really nice job! 🚀

JoseEspinosa · 2022-07-12T14:47:23Z

subworkflows/nf-core/fastqc_fastp.nf

+            .join(trim_json)
+            .map {
+                meta, reads, json ->
+                    if (getFastpReadsAfterFiltering(json) > 0) {


drpatelh · 2022-07-12T16:21:05Z

Thanks for the reviews guys!

Fix #316

drpatelh and others added 30 commits March 4, 2022 15:44

Bump pipeline version to 2.5dev

aea5c83

Merge pull request #293 from drpatelh/bump

12833c4

Bump pipeline version to 2.5dev

Template update for nf-core/tools version 2.3

98aba35

Template update for nf-core/tools version 2.3.1

edd8bb9

Template update for nf-core/tools version 2.3.2

54a3225

Fix merge conflicts

8bb920e

Update CHANGELOG after merging template updates

c7e62dd

Fix template merge bug

5fa2191

Remove TODO statement in README

bd19710

Remove retry logic from AWS actions

952d10a

Add .prettierignore file

3d5c560

Fix ECLint

408b31e

Merge pull request #301 from drpatelh/sync

eb6f554

Update CHANGELOG after merging template updates

Merge branch 'dev' of github.com:BU-ISCIII/viralrecon into dev

8ed4fa6

start reformat

3ef2937

draft reformat

293664e

vcf conversion and strand bias working

fe8adb2

fixed bugs, finished first debugging

2f14d06

black linting

1514898

comments and function reordering

780be42

fix variants iterator

a4067ec

fixed bug in format field and last lines handling

a5a0a40

minor fixed comment

9bff8a5

updated changelog

62d3302

Merge pull request #304 from BU-ISCIII/dev

7c787e0

Re-factor code (proposal) for ivar_variants_to_vcf script

added fasta arg and contig field to vcf header

5d0d14b

fixed filter field

70dceae

installed bcftools sort module

68a05d4

added bcftools sort step in ivar_variants subworkflow

04fceef

removed sorting with awk in ivar_variants_to_vcf module

eb9cf95

drpatelh and others added 23 commits July 7, 2022 11:23

Follow up fix for PR #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

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 #292

a1f810b

Fix #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 #311

cb7efb7

Fix #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

Merge pull request #314 from drpatelh/sync

429a5ff

Update modules and fix bugs for v2.5 release

svarona approved these changes Jul 12, 2022

View reviewed changes

JoseEspinosa approved these changes Jul 12, 2022

View reviewed changes

drpatelh and others added 2 commits July 13, 2022 13:51

Fix #316

f7f8165

Merge pull request #318 from drpatelh/sync

74ee2b6

Fix #316

drpatelh merged commit 3ee1fe9 into master Jul 13, 2022

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Dev -> Master for 2.5 release #315

Dev -> Master for 2.5 release #315

drpatelh commented Jul 12, 2022

github-actions bot commented Jul 12, 2022 •

edited

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

JoseEspinosa left a comment

JoseEspinosa Jul 12, 2022

drpatelh commented Jul 12, 2022

Dev -> Master for 2.5 release #315

Dev -> Master for 2.5 release #315

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drpatelh commented Jul 12, 2022

github-actions bot commented Jul 12, 2022 • edited

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

JoseEspinosa left a comment

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JoseEspinosa Jul 12, 2022

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drpatelh commented Jul 12, 2022

github-actions bot commented Jul 12, 2022 •

edited

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