Pull request for adding compartmentalization analysis by ugoiannacchero · Pull Request #126 · nf-core/sammyseq

ugoiannacchero · 2026-07-25T12:02:20Z

Adding chromatin compartments analysis and mm10 dataset profile test configuration 'test_groups'

PR checklist

…ll mqc bug

…_calling and differential_enrichment modules + some little fixes

nf-core-bot · 2026-07-25T12:03:03Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.4.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

ugoiannacchero · 2026-07-25T12:04:30Z

@nf-core-bot fix linting

daisymut

:O

SPPearce · 2026-07-27T05:45:48Z

            params.bigwigcompare_pseudocount ? "--pseudocount ${params.bigwigcompare_pseudocount}" : '',
            params.bigwigcompare_operation ? "--operation ${params.bigwigcompare_operation}" : '',
            params.bigwigcompare_skip_non_covered_regions ? "--skipNonCoveredRegions" : '',
            params.bigwigcompare_fixed_step ? "--fixedStep" : '',
            "--binSize ${params.bw_resolution}",
            // params.blacklist ? "--blackListFileName ${params.blacklist}" : '',


These seem to be being applied within the Trimgalore process:
https://github.com/nf-core/sammyseq/actions/runs/30158193173/job/89896365673#step:4:651

daisymut · 2026-07-27T11:01:26Z

@nf-core-bot fix linting

github-actions · 2026-07-27T11:17:14Z

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

Posted for pipeline commit 141d023

+| ✅ 216 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   8 tests had warnings |!

Details

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in main.nf.test: Once you have added the required tests, please run the following command to build this file:
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
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 test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ Tests passed:

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files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
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files_exist - File found: assets/sendmail_template.txt
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files_exist - File found: conf/modules.config
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files_exist - File found: .github/workflows/awstest.yml
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files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
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files_exist - File not found check: conf/aws.config
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files_exist - File not found check: lib/Checks.groovy
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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: 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 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 variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
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/
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nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
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nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.trimmer= trimgalore
nextflow_config - Config default value correct: params.aligner= bwamem
nextflow_config - Config default value correct: params.platform= ILLUMINA
nextflow_config - Config default value correct: params.q_score= 1
nextflow_config - Config default value correct: params.flag= 1540
nextflow_config - Config default value correct: params.comparison_maker= spp
nextflow_config - Config default value correct: params.solubility_threshold= 0.1
nextflow_config - Config default value correct: params.igenomes_ignore= true
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes
nextflow_config - Config default value correct: params.corr_method= spearman
nextflow_config - Config default value correct: params.fragment_size= 100
nextflow_config - Config default value correct: params.bw_resolution= 1
nextflow_config - Config default value correct: params.normalizeUsing= RPKM
nextflow_config - Config default value correct: params.numberOfSamples= 500000
nextflow_config - Config default value correct: params.bigwigcompare_pseudocount= 1.0
nextflow_config - Config default value correct: params.bigwigcompare_operation= log2
nextflow_config - Config default value correct: params.bigwigcompare_skip_non_covered_regions= true
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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
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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 - 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-sammyseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-sammyseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-sammyseq_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_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
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actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 25.04.0, Config: 25.04.0
readme - README nf-core template version badge found.
pipeline_if_empty_null - No ifEmpty(null) strings found
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: fix_linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
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merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
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modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
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base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - TRIMMOMATIC found in conf/modules.config and Nextflow scripts.
modules_config - TRIMGALORE found in conf/modules.config and Nextflow scripts.
modules_config - UNTAR_ found in conf/modules.config and Nextflow scripts.
modules_config - DEEPTOOLS_COMPUTEMATRIX_REFERENCE_POINT found in conf/modules.config and Nextflow scripts.
modules_config - DEEPTOOLS_PLOTPROFILE 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: 3.4.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.4.1
Run at 2026-07-27 11:36:19

…ow 25.10.4

ugoiannacchero and others added 30 commits November 20, 2025 11:57

created subworkflow for compartmentalization analysis

dffc34d

created subworkflow for compartmentalization analysis

e5b5a04

implementing compartmentalization analysis

e36f2ae

implementing compartmentalization_analysis

96f369b

update sammyseq workflow

16722a1

update

66550c9

update documentation

1721903

update README

59562c7

update README

234b041

fixing inverted color A/B assignment

1d81ba7

fixing inverted color A/B assignment

667d4db

fixing inverted color A/B assignment

3e082fd

add consensus generation

dc617cd

add consensus generation

277508e

add consensus generation

bc2c8fa

add consensus generation

ca63dc0

add consensus generation

7afb3f8

update

69d2530

new docker + updating compartmentalization analysis

8be8a53

update documentation

f7449a0

update documentation

77690d5

updating rocrate

234aa84

updating metromap

84cc117

Change bigwigcompare_pseudocount to 1

2273fe4

allows the S3vsS2S, S3vsS2L, S3vsS2 comparisons

551d7b4

set pseudocount 1 as suggested my deeptools manual

8b3cf5f

fix prettier

ed06083

remove no coverage

32dce5b

remove bins that have not coverage in one patient

73442db

remove bins that have not coverage in one patient

f95f98a

ugoiannacchero and others added 16 commits July 9, 2026 08:31

add IGV color configuration to combined bedGraph header

516328a

set back to medium

d034677

set back to medium

a5b163b

fixing eigenvector shift

24800a5

added CALDER2 citation

3a5dfe3

default.nf.test snapshot updated

9ec515f

added parameter skip_deeptools_qc to make it optional and fixed a sma…

7351f20

…ll mqc bug

created new multi-arch environment and container for chr_compartments…

a35f6e4

…_calling and differential_enrichment modules + some little fixes

changed to sammyR package

014be2c

removed functions from templates/differential_enrichment.R

95f3a5d

pinned sammyr:0.0.0.9001

9be8aab

run prettier

de3bc3f

fixing test_groups config file

c582652

update snapshot

6275db6

adding correct comparison S2SvsS3

f20daff

update snapshot

ff49d2a

[automated] Fix code linting

68ac3aa

daisymut approved these changes Jul 26, 2026

View reviewed changes

SPPearce reviewed Jul 27, 2026

View reviewed changes

Comment thread conf/modules.config Outdated

SPPearce reviewed Jul 27, 2026

View reviewed changes

ugoiannacchero force-pushed the test_sammyR branch from 768290e to 68ac3aa Compare July 27, 2026 09:08

ci: pin Nextflow to 25.10.4 for linting

64054a9

lint: ignore files_unchanged for linting.yml because we pinned Nextfl…

141d023

…ow 25.10.4

daisymut merged commit aa5def9 into dev Jul 27, 2026
8 checks passed

daisymut linked an issue Jul 27, 2026 that may be closed by this pull request

Add compartment analysis subworkflow and components #57

Closed

daisymut mentioned this pull request Jul 27, 2026

Add compartment analysis subworkflow and components #57

Closed

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Pull request for adding compartmentalization analysis - #126

Pull request for adding compartmentalization analysis#126
daisymut merged 63 commits into
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ugoiannacchero commented Jul 25, 2026

PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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