1.6.1 - Ultra update + Readmapping by DLBPointon · Pull Request #145 · sanger-tol/curationpretext

DLBPointon · 2026-03-18T10:47:52Z

Update for new pretextsnapshot
Update sanger-tol subworkflows:

Update pairs_create_contact_maps
Move to sanger-tol/read_density

Syntax updates
Help now works

github-actions · 2026-03-18T10:51:16Z

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

Posted for pipeline commit 7a6a1d9

+| ✅ 182 tests passed       |+
#| ❔  32 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   3 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.6.1
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: assets/nf-core-curationpretext_logo_light.png
files_exist - File is ignored: docs/images/nf-core-curationpretext_logo_light.png
files_exist - File is ignored: docs/images/nf-core-curationpretext_logo_dark.png
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: CODE_OF_CONDUCT.md
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File does not exist: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/config.yml
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-curationpretext_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-curationpretext_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-curationpretext_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/curationpretext/curationpretext/.github/workflows/awstest.yml
multiqc_config - multiqc_config

❔ Tests fixed:

rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
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: 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/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/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.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: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
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: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: conf/base.config
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-curationpretext_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/WorkflowCurationpretext.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.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
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 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.split_telomere= false
nextflow_config - Config default value correct: params.cram_chunk_size= 10000
nextflow_config - Config default value correct: params.all_output= false
nextflow_config - Config default value correct: params.multi_mapping= 0.0
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/
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml 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
readme - README Nextflow minimum version badge matched config. Badge: 25.04.0, Config: 25.04.0
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
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_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: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: sanger_test_full.yml
actions_schema_validation - Workflow validation passed: sanger_test.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: download_pipeline.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'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - SAMTOOLS_MERGE found in conf/base.config and Nextflow scripts.
base_config - SAMTOOLS_MERGEDUP found in conf/base.config and Nextflow scripts.
base_config - PRETEXT_GRAPH found in conf/base.config and Nextflow scripts.
base_config - BWAMEM2_INDEX found in conf/base.config and Nextflow scripts.
base_config - MINIMAP2_INDEX found in conf/base.config and Nextflow scripts.
base_config - GNU_SORT found in conf/base.config and Nextflow scripts.
base_config - BEDTOOLS_INTERSECT found in conf/base.config and Nextflow scripts.
base_config - TELOMERE_WINDOWS found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - PRETEXT_INGEST_SNDRD found in conf/modules.config and Nextflow scripts.
modules_config - PRETEXTSNAPSHOT found in conf/modules.config and Nextflow scripts.
modules_config - PRETEXTMAP found in conf/modules.config and Nextflow scripts.
modules_config - UCSC_BEDGRAPHTOBIGWIG found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_REPLACE_DOTS found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_RENAME_IDS found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_REFORMAT_INTERSECT found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_GENERATE_GENOME_FILE found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_UPPER_SEQUENCE found in conf/modules.config and Nextflow scripts.
modules_config - GNU_SORT_A found in conf/modules.config and Nextflow scripts.
modules_config - GNU_SORT_B found in conf/modules.config and Nextflow scripts.
modules_config - GNU_SORT_C found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_MAKEWINDOWS found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_INTERSECT found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_MAP found in conf/modules.config and Nextflow scripts.
modules_config - SEQTK_CUTN found in conf/modules.config and Nextflow scripts.
modules_config - PRETEXT_INGEST_SNDRD found in conf/modules.config and Nextflow scripts.
modules_config - PRETEXT_INGEST_HIRES found in conf/modules.config and Nextflow scripts.
modules_config - PRETEXT_INGEST_ULTRA found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - TELOMERE_WINDOWS 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: 3.5.2
rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-03-20 16:27:28

prototaxites

LGTM! One bit of missing documentation

README.md

Updates

be9b009

DLBPointon added 18 commits March 18, 2026 13:52

Updates should fix the help thing

68a7f37

Update version in snap

c4c08b7

Update from sanger-tol

73945ca

Install repeat_density from sanger-tol

b5a1719

Update to include snapshot order file

b64a7d6

Update for sanger-tol/read_density

7f95bab

Update for sanger-tol subworkflow

c94db2f

Update modules

d809535

Update usage docs

733bfaa

Adding Snapshot support

e1226fe

Update docs

47fb750

Add patch for nfschema plugin

cdf73ea

Add patch for nfschema plugin

7caa903

Add snapshotorder to schema

3758796

linting

43b3a92

add patch

ec658d5

update

33227e8

Update and revert a couple of things

148db24

DLBPointon marked this pull request as ready for review March 20, 2026 13:03

DLBPointon added this to WRAP team board Mar 20, 2026

github-project-automation bot moved this to Todo in WRAP team board Mar 20, 2026

DLBPointon changed the title ~~Updates~~ 1.6.1 - Ultra update + Readmapping Mar 20, 2026

prototaxites approved these changes Mar 20, 2026

View reviewed changes

README.md Outdated Show resolved Hide resolved

Add missing docs

7a6a1d9

DLBPointon merged commit bc04469 into dev Mar 21, 2026
7 checks passed

github-project-automation bot moved this from Todo to Done in WRAP team board Mar 21, 2026

DLBPointon deleted the schema_update branch March 21, 2026 20:38

DLBPointon mentioned this pull request Mar 21, 2026

Update subworkflow pairs_create_contact_maps #146

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1.6.1 - Ultra update + Readmapping#145

1.6.1 - Ultra update + Readmapping#145
DLBPointon merged 20 commits intodevfrom
schema_update

DLBPointon commented Mar 18, 2026 •

edited

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github-actions bot commented Mar 18, 2026 •

edited

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❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

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DLBPointon commented Mar 18, 2026 •

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github-actions bot commented Mar 18, 2026 •

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