Release 1.4 #121

fbdtemme · 2024-12-13T14:53:32Z

Release 1.4

[1.4.0] - 2024-12-13

Enhancements & fixes

[PR #111] - Template update for nf-core/tools v3.0.2
[PR #112] - Add graph refinement options for pixelator 0.19
[PR #113] - Fix validation issues after nf-core/tools v3.0.2 update
[PR #114] - Remove --save_recovered_components options for graph outputs
[PR #115] - Update containers for pixelator 0.19
[PR #116] - Bump version to 1.4
[PR #117] - Template update for nf-core/tools v3.1.0
[PR #118] - Update metromap, bump conda versions
[PR #120] - Add process_long to AMPLICON and COLLAPSE steps

Important! Template update for nf-core/tools v3.0.2

Add graph refinement options for pixelator 0.19

Fix validation issues after nf-core/tools v3 template update

…a.json

…overed Remove `--save_recovered_components` options for graph outputs

Update containers for 0.19.0

Bump version for 1.4 release

Important! Template update for nf-core/tools v3.1.0

Update metromap, bump conda versions

Add `process_long` labels to AMPLICON and COLLAPSE

github-actions · 2024-12-13T14:54:58Z

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

Posted for pipeline commit ca529a0

+| ✅ 229 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

pipeline_todos - TODO string in ro-crate-metadata.json: "description": "
\n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-pixelator_logo_dark.png">\n <img alt="nf-core/pixelator" src="docs/images/nf-core-pixelator_logo_light.png">\n \n
\n\n\n \n\n\n\n\n\n\n\n\n \n\n## Introduction\n\nnf-core/pixelator is a bioinformatics pipeline that ...\n\n TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n\n\n Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. \n Fill in short bullet-pointed list of the default steps in the pipeline \n\n\n\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.\n\n Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\nsamplesheet.csv:\n\ncsv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n\n\nNow, you can run the pipeline using:\n\n update the following command to include all required parameters for a minimal example \n\nbash\nnextflow run nf-core/pixelator \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.\n\nFor more details and further functionality, please refer to the usage documentation and the parameter documentation.\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\noutput documentation.\n\n## Credits\n\nnf-core/pixelator was originally written by Pixelgen Technologies AB.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n If applicable, make list of people who have also contributed \n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the contributing guidelines.\n\nFor further information or help, don't hesitate to get in touch on the Slack #pixelator channel (you can join with this invite).\n\n## Citations\n\n Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. \n If you use nf-core/pixelator for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX \n\n Add bibliography of tools and data used in your pipeline \n\nAn extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.\n\nYou can cite the nf-core publication as follows:\n\n> The nf-core framework for community-curated bioinformatics pipelines.\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.\n",
pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
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!
pipeline_todos - TODO string in base.config: Check the defaults for all processes

❔ Tests ignored:

files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_unchanged - File ignored due to lint config: assets/nf-core-pixelator_logo_light.png
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 found: ro-crate-metadata.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 - Found nf-schema plugin
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: validation.help.enabled
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 found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
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 variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
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 manifest.version does not contain dev for release: 1.4.0
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.graph_max_refinement_recursion_depth= 5
nextflow_config - Config default value correct: params.graph_max_edges_to_split= 5
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.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.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 - 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: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 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: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcments.yml
actions_schema_validation - Workflow validation passed: ci.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
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: 3.1.0
version_consistency - Version tags are numeric and consistent between container, release tag and config.
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 3.1.0
Run at 2025-01-03 10:57:48

ambarrio · 2024-12-19T13:17:38Z

Can you give us a hand on this one @mashehu and @avani-bhojwani on a short timeline? Thanks!

avani-bhojwani · 2024-12-21T02:46:35Z

consider updating to version 2.0.0, rather than 1.4.0 since the deprecation of a parameter could justify a major release (https://nf-co.re/docs/guidelines/pipelines/requirements/semantic_versioning#major-release-eg-143-to-200)

avani-bhojwani

Looks good - Just a few questions/changes

nextflow.config

conf/base.config

conf/pixelgen_aws.config

…e.config

fbdtemme · 2025-01-03T11:14:11Z

Since the push to follow semantic versioning more strictly is only from last month, we would like to do this still as a minor release. We will have a v2 following quite soon and can start strict semantic versioning with that version.

sateeshperi

please see comments about local modules. Would also be great if they are unit tested with nf-tests. is this something you can work on adding before release ?

sateeshperi · 2025-01-04T05:07:56Z

CHANGELOG.md

@@ -3,6 +3,51 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

+## [[1.4.0](https://github.com/nf-core/pixelator/releases/tag/1.4.0)] - 2024-12-13


update date before release

sateeshperi · 2025-01-04T05:11:24Z

docs/output.md

@@ -12,6 +12,7 @@ of [`pixelator`](https://github.com/PixelgenTechnologies/pixelator).

 The pipeline consists of the following steps:

+- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution


best to list these steps in the order of execution

sateeshperi · 2025-01-04T05:12:11Z

docs/output.md

-(see `--multiplet_recovery`). These new component IDs are then stored in the "component" column. The information to keep track of the original and
-newly recovered components are stored in a file (components_recovered.csv).
-This file is not included in the output folder by default, but can be included by passing `--save_recovered_components`.
+(see `--multiplet_recovery`). These new component IDs are then stored in the "component" column.


stored in column where ?

sateeshperi · 2025-01-04T05:14:20Z

modules/local/pixelator/collect_metadata.nf


 process PIXELATOR_COLLECT_METADATA {
    label 'process_single'
    cache false

-    conda "bioconda::pixelator=0.18.2"
+    conda "bioconda::pixelator=0.19.0"


best to follow the standard practice of putting the package info in an environment.yml and provide that

sateeshperi · 2025-01-04T05:15:49Z

modules/local/pixelator/collect_metadata.nf

@@ -70,8 +65,7 @@ process PIXELATOR_COLLECT_METADATA {
        parameters: params
    ]

-    def nextflowJson = JsonOutput.toJson(metadata)
-
+    def nextflowJson = groovy.json.JsonOutput.toJson(metadata)


need to collect version info from this module

sateeshperi · 2025-01-04T05:18:28Z

nextflow.config

+    contributors    = [
+        // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
+        [
+            name: 'Pixelgen Technologies AB',


update contributor info

sateeshperi · 2025-01-04T05:19:01Z

nextflow.config

    doi             = '10.1101/2023.06.05.543770'
 }

-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'


don't need modules.config ?

nf-core-bot and others added 30 commits October 8, 2024 12:31

Template update for nf-core/tools version 3.0.0

858d415

Template update for nf-core/tools version 3.0.1

7be24d4

Template update for nf-core/tools version 3.0.2

7ae55f9

Merge branch 'dev' into nf-core-template-merge-3.0.2

a2e141a

Update cat/fastq module

f82e485

Remove duplicated lines form old template

769d9ab

Update logo

6c9acca

Merge pull request #111 from nf-core/nf-core-template-merge-3.0.2

1d0d302

Important! Template update for nf-core/tools v3.0.2

Add graph refinement options and remove unused use_counts

a36aa73

Update CHANGELOG

789abc7

Ignore linting failure on logo

fe74a16

Fix stray space and typo

c644129

Add --max-edges-to-split parameter to CHANGELOG

0e8759f

Fix parameter names in CHANGELOG

c359165

Merge pull request #112 from nf-core/feat/add-graph-refinement-options

95d8eed

Add graph refinement options for pixelator 0.19

Fix validation check after nf-schema 2 update

ad31578

Fix non existence check on input_basedir

3827a3e

Update CHANGELOG

0e7e0c2

Merge pull request #113 from nf-core/fix-panel-file-validation

a2a6c1c

Fix validation issues after nf-core/tools v3 template update

Remove --save_recovered_components options for graph outputs

3067ff3

Remove reference to --save_recovered_components from nextflow_schem…

2b52d00

…a.json

Fix test config defaults

37cc14d

Update help for --dynamic_filter

ed7e5a6

Remove --min-size from test profile

7d6510e

Fix linter warning

55927f8

Merge pull request #114 from nf-core/feat/remove-graph-components-rec…

0777f78

…overed Remove `--save_recovered_components` options for graph outputs

Update images to pixelator 0.19

e0ecbe9

Update nf-core subworkflows

a580cdf

Reduce --min-size filter in test_panel_v2 profile

1811faa

Update CHANGELOG

f6f937d

fbdtemme and others added 16 commits December 11, 2024 11:36

Merge pull request #115 from nf-core/update-containers

e1fd214

Update containers for 0.19.0

Bump version from 1.4.0dev to 1.4.0

1559e09

Template update for nf-core/tools version 3.1.0

f36120b

Merge pull request #116 from nf-core/bump-version

3b80478

Bump version for 1.4 release

Merge branch 'dev' into nf-core-template-merge-3.1.0

dd40572

Sync some nf-core template files

e15a0d1

Fix missing modules.config include

41f8bef

Fix some linter errors

5d7a14b

Merge pull request #117 from nf-core/nf-core-template-merge-3.1.0

c22e520

Important! Template update for nf-core/tools v3.1.0

Update metromap and CHANGELOG

444ec7d

Bump conda versions

c6205e6

Merge pull request #118 from PixelgenTechnologies/update-metromap-v1.4

2593897

Update metromap, bump conda versions

Add process_long labels to AMPLICON and COLLAPSE

e58bee0

Fix CHANGELOG pr number

c5b8472

Merge pull request #120 from PixelgenTechnologies/update-labels

405a62b

Add `process_long` labels to AMPLICON and COLLAPSE

Fix 1.4 version in CHANGELOG

4cdeef6

fix: double singularity pixelator container reference

4072406

ambarrio requested review from avani-bhojwani and mashehu December 19, 2024 13:16

avani-bhojwani requested changes Dec 21, 2024

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fbdtemme added 2 commits January 3, 2025 11:56

Revert move of 'conf/modules.config` from nextflow.config to conf/bas…

4058d84

…e.config

Remove empty config file

ca529a0

fbdtemme requested a review from avani-bhojwani January 3, 2025 11:14

avani-bhojwani approved these changes Jan 4, 2025

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sateeshperi reviewed Jan 4, 2025

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Release 1.4 #121

Release 1.4 #121

fbdtemme commented Dec 13, 2024

github-actions bot commented Dec 13, 2024 •

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❗ Test warnings:

\n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-pixelator_logo_dark.png">\n <img alt="nf-core/pixelator" src="docs/images/nf-core-pixelator_logo_light.png">\n \n

❔ Tests ignored:

✅ Tests passed:

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ambarrio commented Dec 19, 2024

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		@@ -12,6 +12,7 @@ of [`pixelator`](https://github.com/PixelgenTechnologies/pixelator).

		The pipeline consists of the following steps:

		- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution

Release 1.4 #121

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Release 1.4 #121

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fbdtemme commented Dec 13, 2024

[1.4.0] - 2024-12-13

Enhancements & fixes

github-actions bot commented Dec 13, 2024 • edited Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

\n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-pixelator_logo_dark.png">\n <img alt="nf-core/pixelator" src="docs/images/nf-core-pixelator_logo_light.png">\n \n

❔ Tests ignored:

✅ Tests passed:

Run details

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github-actions bot commented Dec 13, 2024 •

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