Release 1.1.0 #33

carpanz · 2023-05-12T14:00:55Z

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).

…flow config

Modules update and bugs fix

forgot to update samtools version in local module and CHANGELOG

Modules update and bug fix

github-actions · 2023-05-12T14:06:22Z

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

Posted for pipeline commit 115bd96

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

❗ Test warnings:

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

✅ Tests passed:

files_exist - File found: .gitattributes
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files_exist - File found: CITATIONS.md
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files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
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files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
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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/
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nextflow_config - Lines for loading custom profiles found
files_unchanged - .gitattributes matches the template
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files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
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files_unchanged - assets/nf-core-hgtseq_logo_light.png matches the template
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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 2023-05-15 10:52:41

lescai

Reviewed in dev already.
Code looks good to me, all checks are passed.
Important to release the bug fix. This is also a chance to sync the pipeline to latest version of modules and software as well as to strengthen documentation.

FriederikeHanssen

Almost there 🚀

modules/local/samtools/viewsingle/main.nf

nextflow.config

Fixed as suggested in review

FriederikeHanssen

🚀 great work

nf-core-bot and others added 30 commits October 4, 2022 21:53

Template update for nf-core/tools version 2.6

ab2b29b

bumped new version on dev

8029489

Merge pull request #25 from carpanz/dev

1fabb33

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

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

added map to fasta input

2d77bf8

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

carpanz and others added 20 commits May 10, 2023 12:11

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

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

Merge pull request #31 from carpanz/dev

077e54b

Modules update and bug fix

carpanz requested review from lescai and FriederikeHanssen May 12, 2023 14:16

lescai approved these changes May 12, 2023

View reviewed changes

FriederikeHanssen requested changes May 13, 2023

View reviewed changes

modules/local/samtools/viewsingle/main.nf Outdated Show resolved Hide resolved

nextflow.config Outdated Show resolved Hide resolved

carpanz and others added 2 commits May 15, 2023 12:07

fixed as suggested in review

5d1f56f

Merge pull request #34 from carpanz/dev

115bd96

Fixed as suggested in review

carpanz requested a review from FriederikeHanssen May 15, 2023 11:02

FriederikeHanssen approved these changes May 15, 2023

View reviewed changes

lescai merged commit 683daaf into master May 16, 2023

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Release 1.1.0 #33

Release 1.1.0 #33

carpanz commented May 12, 2023

github-actions bot commented May 12, 2023 •

edited

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❗ Test warnings:

✅ Tests passed:

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lescai left a comment

FriederikeHanssen left a comment

FriederikeHanssen left a comment

Release 1.1.0 #33

Release 1.1.0 #33

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carpanz commented May 12, 2023

PR checklist

github-actions bot commented May 12, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

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github-actions bot commented May 12, 2023 •

edited

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