Release 1.2.0 #49

christopher-mohr · 2023-08-24T06:24:04Z

Release PR for v1.2.0.

Solves Fix unique colnames requirement for heatmap #39 , NACHO (qc) report not published #44 and Update NACHO R package #45.
Update to template 2.9

PR checklist

Allow normalization adjustment

… update_fix_issues

Co-authored-by: Gregor Sturm <[email protected]>

Update template, fix issue

Update container

Add parameter to specify id column for heatmap

github-actions · 2023-08-24T06:25:54Z

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

Posted for pipeline commit b193b16

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.2.0

✅ 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-nanostring_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-nanostring_logo_light.png
files_exist - File found: docs/images/nf-core-nanostring_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/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/WorkflowNanostring.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-nanostring_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.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
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-nanostring_logo_light.png matches the template
files_unchanged - docs/images/nf-core-nanostring_logo_light.png matches the template
files_unchanged - docs/images/nf-core-nanostring_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/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: 23.04.0, Config: 23.04.0
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 (86 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: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: fix-linting.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
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 2.9
Run at 2023-09-01 06:51:56

CHANGELOG.md

nextflow.config

assets/multiqc_config.yml

update version

modules/local/create_gene_heatmap.nf

modules/local/nacho/normalize.nf

nextflow.config

workflows/nanostring.nf

Fix normalization & address PR comments

nf-core-bot and others added 30 commits March 24, 2022 11:42

Template update for nf-core/tools version 2.3.2

22ddf0d

Template update for nf-core/tools version 2.4

73c61f1

Template update for nf-core/tools version 2.5

fcbb9d9

Template update for nf-core/tools version 2.5.1

2268123

Template update for nf-core/tools version 2.6

6ed106a

Template update for nf-core/tools version 2.7.1

044c200

Template update for nf-core/tools version 2.7.2

034aa3f

Template update for nf-core/tools version 2.8

ba9dc71

Allow adjusting normalization parameters

4f09c80

Add usage

c485a5f

Prettier

3f9efe8

Update CHANGELOG.md

de10667

Merge pull request #42 from nf-core/allow-normalization-adjustment

9f4a05d

Allow normalization adjustment

Template update for nf-core/tools version 2.9

6423a8f

Merge branch 'TEMPLATE' of https://github.com/nf-core/nanostring into…

9ab706f

… update_fix_issues

update CHANGELOG

f2c574a

add NACHO reports to published files

244c53e

add PR number to CHANGELOG

a5849a9

update nf-core modules

0a89188

Update docs/usage.md

e71e937

Co-authored-by: Gregor Sturm <[email protected]>

Update docs/usage.md

00a5e42

Co-authored-by: Gregor Sturm <[email protected]>

run prettier

9b59810

correct PR number

aed2394

Merge pull request #46 from christopher-mohr/update_fix_issues

0551625

Update template, fix issue

update mulled container

6f92a4d

update CHANGELOG

5de6f52

update container, conda string

399cee0

update CHANGELOG

89a72cd

Merge pull request #47 from christopher-mohr/update_container

84ff170

Update container

add parameter for specifying id column for heatmap

bafa2ca

christopher-mohr added 2 commits August 21, 2023 09:11

use correct PR numbers

2f90252

Merge pull request #48 from christopher-mohr/add_params

390fe60

Add parameter to specify id column for heatmap

christopher-mohr commented Aug 24, 2023

View reviewed changes

CHANGELOG.md Outdated Show resolved Hide resolved

christopher-mohr commented Aug 24, 2023

View reviewed changes

nextflow.config Outdated Show resolved Hide resolved

christopher-mohr commented Aug 24, 2023

View reviewed changes

assets/multiqc_config.yml Outdated Show resolved Hide resolved

christopher-mohr commented Aug 24, 2023

View reviewed changes

assets/multiqc_config.yml Outdated Show resolved Hide resolved

christopher-mohr and others added 2 commits August 24, 2023 13:51

update version

71b70d2

Merge pull request #50 from christopher-mohr/update_version

da69703

update version

apeltzer approved these changes Aug 30, 2023

View reviewed changes

maxulysse reviewed Aug 30, 2023

View reviewed changes

modules/local/create_gene_heatmap.nf Outdated Show resolved Hide resolved

maxulysse reviewed Aug 30, 2023

View reviewed changes

modules/local/nacho/normalize.nf Outdated Show resolved Hide resolved

maxulysse reviewed Aug 30, 2023

View reviewed changes

nextflow.config Outdated Show resolved Hide resolved

maxulysse reviewed Aug 30, 2023

View reviewed changes

workflows/nanostring.nf Show resolved Hide resolved

christopher-mohr added 4 commits August 31, 2023 08:25

apply review suggestions

a5f598d

make heatmap_gene_filter_file input channel

327dd8e

use norm method for non-hk -norm, no hk-norm

2297e23

update CHANGELOG

f9e4125

christopher-mohr mentioned this pull request Sep 1, 2023

Fix normalization & address PR comments #51

Merged

10 tasks

christopher-mohr and others added 3 commits September 1, 2023 06:41

update CHANGELOG

0891258

remove print statement

84af8f5

Merge pull request #51 from christopher-mohr/address_PR_comments

b193b16

Fix normalization & address PR comments

maxulysse approved these changes Sep 4, 2023

View reviewed changes

christopher-mohr merged commit 415bc68 into master Sep 4, 2023
13 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Release 1.2.0 #49

Release 1.2.0 #49

christopher-mohr commented Aug 24, 2023 •

edited

Loading

github-actions bot commented Aug 24, 2023 •

edited

Loading

❗ Test warnings:

✅ Tests passed:

Run details

Release 1.2.0 #49

Release 1.2.0 #49

Conversation

christopher-mohr commented Aug 24, 2023 • edited Loading

PR checklist

github-actions bot commented Aug 24, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

christopher-mohr commented Aug 24, 2023 •

edited

Loading

github-actions bot commented Aug 24, 2023 •

edited

Loading

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