Release nf-core/pixelator 1.2.0 #94

fbdtemme · 2024-05-28T08:33:47Z

Dev -> Master for 1.2.0 release

…ate-to-pixelator-0.17.1 Feature/exe 1732 update to pixelator 0.17.1

…ss-high-to-use-64gb-ram process_high->64GB ram/process_high_memory->128GB

Minor documentation fixes

Important! Template update for nf-core/tools v2.14.1

Improve read renaming

github-actions · 2024-05-28T08:35:20Z

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

Posted for pipeline commit 9bf3bf1

+| ✅ 201 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.2.0
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: conf/igenomes.config
multiqc_config - multiqc_config

✅ 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: 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-pixelator_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-pixelator_logo_light.png
files_exist - File found: docs/images/nf-core-pixelator_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: 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: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
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: docs/images/nf-core-pixelator_logo.png
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/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowPixelator.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
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
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.trim_front= 0
nextflow_config - Config default value correct: params.trim_tail= 0
nextflow_config - Config default value correct: params.max_n_bases= 0
nextflow_config - Config default value correct: params.avg_qual= 20
nextflow_config - Config default value correct: params.adapterqc_mismatches= 0.1
nextflow_config - Config default value correct: params.demux_mismatches= 0.1
nextflow_config - Config default value correct: params.algorithm= adjacency
nextflow_config - Config default value correct: params.max_neighbours= 60
nextflow_config - Config default value correct: params.collapse_mismatches= 2
nextflow_config - Config default value correct: params.collapse_min_count= 2
nextflow_config - Config default value correct: params.multiplet_recovery= true
nextflow_config - Config default value correct: params.leiden_iterations= 10
nextflow_config - Config default value correct: params.graph_min_count= 2
nextflow_config - Config default value correct: params.dynamic_filter= min
nextflow_config - Config default value correct: params.aggregate_calling= true
nextflow_config - Config default value correct: params.compute_polarization= true
nextflow_config - Config default value correct: params.compute_colocalization= true
nextflow_config - Config default value correct: params.polarization_transformation= log1p
nextflow_config - Config default value correct: params.polarization_n_permutations= 50
nextflow_config - Config default value correct: params.polarization_min_marker_count= 5
nextflow_config - Config default value correct: params.colocalization_transformation= log1p
nextflow_config - Config default value correct: params.colocalization_neighbourhood_size= 1
nextflow_config - Config default value correct: params.colocalization_n_permutations= 50
nextflow_config - Config default value correct: params.colocalization_min_region_count= 5
nextflow_config - Config default value correct: params.no_node_marker_counts= false
nextflow_config - Config default value correct: params.layout_algorithm= pmds_3d
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
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-pixelator_logo_light.png matches the template
files_unchanged - docs/images/nf-core-pixelator_logo_light.png matches the template
files_unchanged - docs/images/nf-core-pixelator_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore 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_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (98 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: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: release-announcments.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - PIXELATOR found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_LIST_OPTIONS found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTQ found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_AMPLICON found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_QC found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_DEMUX found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_COLLAPSE found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_GRAPH found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_ANNOTATE found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_ANALYSIS found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_LAYOUT found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_REPORT found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-05-28 11:15:12

CHANGELOG.md

conf/test.config

maxulysse

Looks pretty straight forward to me

ramprasadn

LGTM 🚀

Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>

fbdtemme · 2024-05-28T11:47:58Z

Thanks everyone for the reviews!

nf-core-bot and others added 29 commits May 8, 2024 14:00

Template update for nf-core/tools version 2.14.0

50cb5d7

Template update for nf-core/tools version 2.14.1

796c414

Merge branch 'dev' into nf-core-template-merge-2.14.1

0ab9f89

Merge branch 'dev' into nf-core-template-merge-2.14.1

39c9fd9

Update to use pixelator 0.17.1, add layout command

70fe195

Make graph step use process_high resource

e7d1d58

Formatting fix

99275c6

Skip layout in small test config

edab0dd

Clean-up

4a28425

Update changelog

07b0500

Fix linting issue

1d2fcde

Pass layout to the report stage

bd29d2c

Fix copy-paste-error

1db4263

annotate step use process_high resources

ce90f8b

Clean-up the changelog a bit

1e557b2

Merge pull request #90 from PixelgenTechnologies/feature/exe-1732-upd…

7a769d9

…ate-to-pixelator-0.17.1 Feature/exe 1732 update to pixelator 0.17.1

process_high->64GB ram/process_high_memory->128GB

c41065b

Update changelog

71b413c

Merge pull request #91 from PixelgenTechnologies/feature/change-proce…

c085f75

…ss-high-to-use-64gb-ram process_high->64GB ram/process_high_memory->128GB

Minor documenation fixes

f1b288c

Merge pull request #92 from PixelgenTechnologies/chore/minor-doc-fixes

db761d1

Minor documentation fixes

Merge branch 'dev' into nf-core-template-merge-2.14.1

4a1b1ed

Fix template merge issues

48dbe62

Remove some old nf-core lint opt-outs

64375e9

Merge pull request #89 from nf-core/nf-core-template-merge-2.14.1

f0bc911

Important! Template update for nf-core/tools v2.14.1

Merge RENAME_READS module functionality into PIXELATOR_AMPLICON

ea9548c

Update CHANGELOG

ca85ee4

Remove RENAME_READS from modules.config

6407896

Merge pull request #93 from PixelgenTechnologies/improve-read-renaming

7e470cc

Improve read renaming

johandahlberg reviewed May 28, 2024

View reviewed changes

CHANGELOG.md Outdated Show resolved Hide resolved

maxulysse reviewed May 28, 2024

View reviewed changes

conf/test.config Outdated Show resolved Hide resolved

maxulysse approved these changes May 28, 2024

View reviewed changes

ramprasadn approved these changes May 28, 2024

View reviewed changes

fbdtemme and others added 2 commits May 28, 2024 13:08

Update conf/test.config

a2b315e

Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>

Update release date in CHANGELOG

9bf3bf1

fbdtemme merged commit 35c594f into master May 28, 2024
11 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Release nf-core/pixelator 1.2.0 #94

Release nf-core/pixelator 1.2.0 #94

fbdtemme commented May 28, 2024

github-actions bot commented May 28, 2024 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse left a comment

ramprasadn left a comment

fbdtemme commented May 28, 2024

Release nf-core/pixelator 1.2.0 #94

Release nf-core/pixelator 1.2.0 #94

Conversation

fbdtemme commented May 28, 2024

github-actions bot commented May 28, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse left a comment

Choose a reason for hiding this comment

ramprasadn left a comment

Choose a reason for hiding this comment

fbdtemme commented May 28, 2024

github-actions bot commented May 28, 2024 •

edited

Loading

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