Modules update and bug fix #31

carpanz · 2023-03-28T14:49:38Z

In this PR we include:

Template and nf-core/modules update to the latest version
Addition of Krona and Circos plot as example to documentation
Addition of local module samtools/viewsingle. When extracting reads, we noticed that also some both_unmapped reads were collected in single_unmapped reads due to a conflict between flags option. In order to resolve this issue, we create a local module where we execute the extraction in two step (i.e. we combine two command with a pipe) instead of running the module twice, which would otherwise be inefficient.

PR checklist

This comment contains a description of changes (with reason).
If you've fixed a bug or added code that should be tested, add tests!
If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/hgtseq branch on the nf-core/test-datasets repository.
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

Release PR 1.0.0

Last changes to release 1.0.0

github-actions · 2023-03-28T17:00:19Z

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

Posted for pipeline commit c74e31c

+| ✅ 159 tests passed       |+
!| ❗   1 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '1.1.0'

✅ 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: assets/nf-core-hgtseq_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-hgtseq_logo_light.png
files_exist - File found: docs/images/nf-core-hgtseq_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: assets/multiqc_config.yml
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/WorkflowHgtseq.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-hgtseq_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.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.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 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/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-hgtseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-hgtseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-hgtseq_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 - lib/NfcoreTemplate.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml 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
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (126 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.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
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
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 2023-05-12 12:55:36

…flow config

Modules update and bugs fix

forgot to update samtools version in local module and CHANGELOG

lescai

All tests passed.
Code reviewed during development.
Only warning related to this being in preparation of minor release.
Good to go for me!

nf-core-bot and others added 12 commits October 4, 2022 21:53

Template update for nf-core/tools version 2.6

ab2b29b

Merge pull request #16 from nf-core/dev

fa9b7c1

Release PR 1.0.0

Merge pull request #23 from nf-core/dev

4cd916f

Last changes to release 1.0.0

Added Zenodo DOI

8965f5b

Updated Citations with Zenodo DOI

f567b2f

FIxed prettier check

800c861

fixed prettier remaining check

67ec450

Template update for nf-core/tools version 2.7.1

9c8496b

Template update for nf-core/tools version 2.7.2

b9d0199

Template update for nf-core/tools version 2.7.dev0

c7858ac

Merge branch 'master' into dev

680f809

added local module samtools/viewsingle

c77854f

carpanz added 17 commits March 29, 2023 09:45

fixed args in new module

b3fb38f

updating samtools view nf-core module

8c626bc

resolving linting problems

246c5ae

fixed files unchanged

7be8ffa

temporary fix for params.enable_conda

f31ad8b

prettier check

ac4d192

Template update for nf-core/tools version 2.7.2

96885c1

Template update for nf-core/tools version 2.7.dev0

b520bbf

resolving conflicts for template update

99fcbb3

resolving conflicts for template update

23445f1

resolving conflicts for template update

ee9a870

removed and changed params.enable_conda

a84b925

removed and changed params.enable_conda

7d16e52

removed params.enable_conda

74ca4d3

started to update modules

c0f5b40

resolved lint warnings and added publication in CITATIONS file

88c0c7d

added map to fasta input

726fef2

carpanz and others added 17 commits May 8, 2023 15:12

added map to fasta input

9d12d69

modified baseName as reported in new version

3ce2a75

modified baseName as reported in new version

abdc77a

updated last modules and removed hard coded trimgalore params in next…

9fee922

…flow config

removed trimgalore hard coded params from json schema

dbeb19c

some corrections in documentation

7e2f6b9

some corrections in documentation

6228ed6

some corrections in documentation

b173d52

added circos plot example to output documentation

4de0691

fixed images dimentions

f505d14

fixed images dimentions

e2b48b1

updated manually samtools/fastq module

6e6f941

fixed new graphs

b82040f

fixed new graphs

d14d8c1

fixed new graphs

3c8902a

forced installation fo samtools/fastq due to linting error

ec3a692

Merge pull request #1 from carpanz/modules_update

e652bea

Modules update and bugs fix

carpanz changed the title ~~Added new local module to fix small bug~~ Modules update and bug fix May 12, 2023

carpanz and others added 8 commits May 12, 2023 13:57

forgot to update samtools version in local module

b56762d

Merge pull request #2 from carpanz/modules_update

98c1e78

forgot to update samtools version in local module and CHANGELOG

fixed changelog

7bac8fe

fixed changelog

52b167d

bumped version e complete release checklist

96baff7

bumped version e complete release checklist

baf9a80

bumped version e completed release checklist

a8cb42e

bumped new version and completed release checklist

c74e31c

carpanz requested a review from lescai May 12, 2023 13:26

lescai approved these changes May 12, 2023

View reviewed changes

lescai merged commit 077e54b into nf-core:dev May 12, 2023

carpanz mentioned this pull request May 12, 2023

Important! Template update for nf-core/tools v2.8 #32

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

Modules update and bug fix #31

Modules update and bug fix #31

Uh oh!

carpanz commented Mar 28, 2023 •

edited

Loading

Uh oh!

github-actions bot commented Mar 28, 2023 •

edited

Loading

❗ Test warnings:

✅ Tests passed:

Run details

Uh oh!

lescai left a comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

Modules update and bug fix #31

Modules update and bug fix #31

Uh oh!

Conversation

carpanz commented Mar 28, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

PR checklist

Uh oh!

github-actions bot commented Mar 28, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

Uh oh!

lescai left a comment

Choose a reason for hiding this comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

carpanz commented Mar 28, 2023 •

edited

Loading

github-actions bot commented Mar 28, 2023 •

edited

Loading

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