Release pixelator 1.3.0 #106

fbdtemme · 2024-07-15T09:29:09Z

Description

[1.3.0] - 2024-07-15

Enhancements & fixes

[PR #97] - Update citations
[PR #96] - Make all ext.args assignments closures
[PR #98] - Update metromap to include layout step
[PR #99] - Update README to include layout step
[PR #100] - Use R1/R2 suffixes in amplicon input fastq file renaming
[PR #101] - Fix validation issue when using panel_file instead of panel
[PR #102] - Restructure output directory
[PR #103] - Make rate-diff the default transformation method when computing colocalization
[PR #104] - Update to pixelator 0.18.1

Software dependencies

Dependency	Old version	New version
`pixelator`	0.17.1	0.18.1

NB: Dependency has been updated if both old and new version information is present.

NB: Dependency has been added if just the new version information is present.

NB: Dependency has been removed if new version information isn't present.

chore: sync dev after release and bump to 1.3.0dev

…osures Make `task.ext` assigments closures

Update metromap to include layout step

Update citations

Chore/update readme

This ensures limited backward compatibility when using the pipeline with older pixelator containers (<0.17) using the `--pixelator_container` flag.

…ming Use R1/R2 suffixes in amplicon input fastq file renaming

A map access error occurs because the meta map gets overwritten with null in validate_panel when no panel key is present. We need to return the meta map unmodified instead.

Fix validation issue when using panel_file instead of panel

Co-authored-by: Alvaro Martinez Barrio <Alvaro.Martinez.Barrio@pixelgen.com> Update docs/output.md Co-authored-by: Alvaro Martinez Barrio <Alvaro.Martinez.Barrio@pixelgen.com> Update docs/output.md Co-authored-by: Alvaro Martinez Barrio <Alvaro.Martinez.Barrio@pixelgen.com> Update docs/output.md Co-authored-by: Alvaro Martinez Barrio <Alvaro.Martinez.Barrio@pixelgen.com> Update docs/output.md Co-authored-by: Alvaro Martinez Barrio <Alvaro.Martinez.Barrio@pixelgen.com> Update docs/output.md Co-authored-by: Alvaro Martinez Barrio <Alvaro.Martinez.Barrio@pixelgen.com> Apply suggestions from code review Co-authored-by: Alvaro Martinez Barrio <Alvaro.Martinez.Barrio@pixelgen.com>

Restructure output folder

…ult-colocalization-transformation Make rate diff default colocalization transformation

…18.0 Update pixelator to 0.18.1

Bump version to 1.3.0

github-actions · 2024-07-15T09:30:30Z

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

Posted for pipeline commit a5247ba

+| ✅ 215 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.3.0
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
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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
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files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
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files_exist - File not found check: .yamllint.yml
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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.save_amplicon_reads= false
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.save_qc_passed_reads= false
nextflow_config - Config default value correct: params.save_qc_failed_reads= false
nextflow_config - Config default value correct: params.demux_mismatches= 0.1
nextflow_config - Config default value correct: params.save_demux_processed_reads= false
nextflow_config - Config default value correct: params.save_demux_failed_reads= false
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.save_collapsed_reads= false
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.save_edgelist= false
nextflow_config - Config default value correct: params.save_recovered_components= false
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.save_raw_component_metrics= false
nextflow_config - Config default value correct: params.save_annotate_dataset= false
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= rate-diff
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.colocalization_min_marker_count= 5
nextflow_config - Config default value correct: params.save_analysis_dataset= false
nextflow_config - Config default value correct: params.no_node_marker_counts= false
nextflow_config - Config default value correct: params.layout_algorithm= wpmds_3d
nextflow_config - Config default value correct: params.save_all= false
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
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files_unchanged - .github/.dockstore.yml matches the template
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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 (99 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: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
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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_COLLECT_METADATA 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 2024-07-17 08:53:05

mashehu

some smaller things, rest looks good 👍🏻

CHANGELOG.md

README.md

conf/test_v2.config

nextflow.config

nextflow_schema.json

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

avani-bhojwani

looks good to me too!

conf/test_panel_v2.config

nextflow_schema.json

Fix some typos and inconsistencies in the docs Co-authored-by: avani-bhojwani <68935109+avani-bhojwani@users.noreply.github.com>

Co-authored-by: avani-bhojwani <68935109+avani-bhojwani@users.noreply.github.com>

fbdtemme · 2024-07-17T09:13:29Z

Thanks @mashehu and @avani-bhojwani for the reviews!

fbdtemme and others added 30 commits May 29, 2024 17:40

chore: bump to 1.3.0dev

a13c0df

Add new changelog entry for dev version

559d95a

Merge pull request #95 from nf-core/sync-dev-after-1.2.0

2252db1

chore: sync dev after release and bump to 1.3.0dev

Make all ext.args assignments closures

56da1fd

Update CHANGELOG

ccb35d0

Merge pull request #96 from PixelgenTechnologies/fix/make-task-ext-cl…

27c8743

…osures Make `task.ext` assigments closures

Update citations

f920319

Update CHANGELOG

1cb639d

Update metromap to include layout step

c320307

Update CHANGELOG

20496c1

Merge pull request #98 from PixelgenTechnologies/update-metromap

31e3dc5

Update metromap to include layout step

fix: add layour docs to readme

98238c8

fix: changelog

141642a

fix: update output layout step

bfe93c4

Merge pull request #97 from PixelgenTechnologies/update-publication

0093847

Update citations

Merge pull request #99 from PixelgenTechnologies/chore/update-readme

12e795c

Chore/update readme

Use R1/R2 suffixes in amplicon input fastq file renaming

ca32765

This ensures limited backward compatibility when using the pipeline with older pixelator containers (<0.17) using the `--pixelator_container` flag.

Merge pull request #100 from PixelgenTechnologies/tweak-amplicon-rena…

9ea493a

…ming Use R1/R2 suffixes in amplicon input fastq file renaming

Fix validation issue when using panel_file instead of panel

dd34553

A map access error occurs because the meta map gets overwritten with null in validate_panel when no panel key is present. We need to return the meta map unmodified instead.

Merge pull request #101 from PixelgenTechnologies/fix-panel-file

dbaec78

Fix validation issue when using panel_file instead of panel

Restructure output directory

97bd99d

Update CHANGELOG

6ddf209

Fix bad pattern for graph/*edgelist.parquet'

d16b018

Use explicit return null in saveAs closures

bead999

Make fastq file reference all caps

4f1de61

Tweak graph stage output description

af797e5

Tweak collapse output description

3516031

Merge pull request #102 from PixelgenTechnologies/restructure-output

6ea4395

Restructure output folder

rate-diff is now default colocalization transform

115c87d

johandahlberg and others added 12 commits July 8, 2024 15:28

Merge pull request #103 from PixelgenTechnologies/make-rate-diff-defa…

51a9ec9

…ult-colocalization-transformation Make rate diff default colocalization transformation

Add colocalization_min_marker_count parameter

faec0f4

Change default layout algorithm to wpmds_3d

6acc037

Update pixelator container to 0.18 using override param

a136ed0

Add v2 panel small test profile

cadf011

Update pixelator container to 0.18.1

96bd927

Update CHANGELOG.md

e9e9035

Remove unused parameter from test_v2.config

b47a4bd

Add human-sc-immunology-spatial-proteomics-2 panel in docs

3790c92

Merge pull request #104 from PixelgenTechnologies/update-pixelator-0.…

79ef889

…18.0 Update pixelator to 0.18.1

Bump version to 1.3.0

2fd30b3

Merge pull request #105 from PixelgenTechnologies/release-1.3

8c3a705

Bump version to 1.3.0

mashehu approved these changes Jul 15, 2024

View reviewed changes

fbdtemme and others added 7 commits July 15, 2024 14:35

Apply suggestions from code review

ed4f50f

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Rename test_v2 to test_panel_v2 and align

b262018

Use edge list instead of edgelist in docs

3de2f54

Output preqc html reports with --save_all

12a2aa9

Align code in nextflow.config

42c0653

Update test_panel_v2 usage comment

d701a59

Fix tubemap icon alignment, add pipeline version

44fc31d

avani-bhojwani self-requested a review July 16, 2024 09:27

avani-bhojwani approved these changes Jul 16, 2024

View reviewed changes

fbdtemme and others added 5 commits July 16, 2024 14:29

Apply suggestions from code review

bc8526a

Fix some typos and inconsistencies in the docs Co-authored-by: avani-bhojwani <68935109+avani-bhojwani@users.noreply.github.com>

Update nextflow_schema.json

ff3ab07

Co-authored-by: avani-bhojwani <68935109+avani-bhojwani@users.noreply.github.com>

Fix input paths to testdata in test_panel_v2 config

fdbd34d

Update to pixelator 0.18.2

3ffd206

Update release date in CHANGELOG

a5247ba

fbdtemme merged commit bf49230 into master Jul 17, 2024
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Release pixelator 1.3.0 #106

Release pixelator 1.3.0 #106

fbdtemme commented Jul 15, 2024

github-actions bot commented Jul 15, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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avani-bhojwani left a comment

fbdtemme commented Jul 17, 2024

Release pixelator 1.3.0 #106

Release pixelator 1.3.0 #106

Conversation

fbdtemme commented Jul 15, 2024

Description

[1.3.0] - 2024-07-15

Enhancements & fixes

Software dependencies

github-actions bot commented Jul 15, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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fbdtemme commented Jul 17, 2024

github-actions bot commented Jul 15, 2024 •

edited

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