Release version 1.1.3 #237

heuermh · 2025-01-30T16:30:29Z

PR checklist

bump to 1.2.0dev

update workflow svg

Merging template updates for versions 2.14.0 through 3.1.1

Update nf-core/smoothxg module to version 0.8.0

make parameter `n_haplotypes` null

…angenome into odgi-0.9.0

Co-authored-by: Friederike Hanssen <[email protected]>

update pggb docker to contain vg v1.62

Refactor authors to list of contributors

…0.9.0

Update nf-core odgi modules to version 0.9.0

Important! Template update for nf-core/tools v3.2.0

prepare new release 1.1.3 - marsupial

heuermh · 2025-01-30T16:43:15Z

Attempting to resolve merge conflicts in #238

Resolve merge conflicts

github-actions · 2025-01-30T17:19:31Z

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

Posted for pipeline commit 1fcf24e

+| ✅ 235 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
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!
local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - pggb.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - odgi_qc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - community.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

files_unchanged - File ignored due to lint config: assets/nf-core-pangenome_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-pangenome_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-pangenome_logo_dark.png

✅ 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-pangenome_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-pangenome_logo_light.png
files_exist - File found: docs/images/nf-core-pangenome_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: assets/multiqc_config.yml
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-pangenome_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/WorkflowPangenome.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: 1.1.3
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.wfmash_map_pct_id= 90.0
nextflow_config - Config default value correct: params.wfmash_segment_length= 5000
nextflow_config - Config default value correct: params.wfmash_mash_kmer= 19
nextflow_config - Config default value correct: params.wfmash_mash_kmer_thres= 0.001
nextflow_config - Config default value correct: params.wfmash_sparse_map= 1.0
nextflow_config - Config default value correct: params.wfmash_chunks= 1
nextflow_config - Config default value correct: params.wfmash_hg_filter_ani_diff= 30
nextflow_config - Config default value correct: params.seqwish_min_match_length= 23
nextflow_config - Config default value correct: params.seqwish_transclose_batch= 10000000
nextflow_config - Config default value correct: params.seqwish_sparse_factor= 0.0
nextflow_config - Config default value correct: params.smoothxg_max_path_jump= 0
nextflow_config - Config default value correct: params.smoothxg_max_edge_jump= 0
nextflow_config - Config default value correct: params.smoothxg_poa_length= 700,900,1100
nextflow_config - Config default value correct: params.smoothxg_block_ratio_min= 0
nextflow_config - Config default value correct: params.smoothxg_pad_max_depth= 100
nextflow_config - Config default value correct: params.smoothxg_poa_padding= 0.001
nextflow_config - Config default value correct: params.smoothxg_poa_params= 1,19,39,3,81,1
nextflow_config - Config default value correct: params.smoothxg_consensus_prefix= Consensus_
nextflow_config - Config default value correct: params.smoothxg_poa_cpus= 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.max_multiqc_email_size= 25.MB
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/
nextflow_config - Config default value correct: params.schema_ignore_params= igenomes_base
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/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/plain'
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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
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
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
local_component_structure - local modules directory structure is correct 'modules/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - WFMASH_MAP_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - WFMASH_MAP found in conf/modules.config and Nextflow scripts.
modules_config - WFMASH_MAP_COMMUNITY found in conf/modules.config and Nextflow scripts.
modules_config - SPLIT_APPROX_MAPPINGS_IN_CHUNKS found in conf/modules.config and Nextflow scripts.
modules_config - WFMASH_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - SEQWISH found in conf/modules.config and Nextflow scripts.
modules_config - SMOOTHXG found in conf/modules.config and Nextflow scripts.
modules_config - GFAFFIX found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_BUILD found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_UNCHOP found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_SORT found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_VIEW found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_STATS found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_VIZ_COLOR found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_VIZ_POS found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_VIZ_DEPTH found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_VIZ_INV found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_VIZ_UNCALLED found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_VIZ_COMPR found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_LAYOUT found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_DRAW_MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_DRAW_HEIGHT found in conf/modules.config and Nextflow scripts.
modules_config - VG_DECONSTRUCT found in conf/modules.config and Nextflow scripts.
modules_config - PAF2NET found in conf/modules.config and Nextflow scripts.
modules_config - NET2COMMUNITIES found in conf/modules.config and Nextflow scripts.
modules_config - EXTRACT_COMMUNITIES found in conf/modules.config and Nextflow scripts.
modules_config - TABIX_BGZIP found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC_COMMUNITY found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_SQUEEZE 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: 3.2.0
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 3.2.0
Run at 2025-01-31 07:21:18

subwaystation · 2025-01-30T20:07:35Z

The linter seems wrong here?! In

pangenome/nextflow.config

Line 106 in d292756

includeConfig 'conf/base.config'

the line is uncommented. Or where else does the linter look? The link to the specification is broken and gives a 404.
@mashehu Maybe you have an idea?

heuermh · 2025-01-31T02:07:46Z

Got help on Slack, fix is in #239

heuermh · 2025-01-31T02:08:16Z

I don't understand this failure though
https://github.com/nf-core/pangenome/actions/runs/13057631753/job/36433443182?pr=237

Fix 1.1.3 release lint error(s)

subwaystation · 2025-01-31T07:21:04Z

I don't understand this failure though https://github.com/nf-core/pangenome/actions/runs/13057631753/job/36433443182?pr=237

Me neither.....

subwaystation and others added 30 commits March 25, 2024 16:12

bump to 1.2.0dev

2ffef33

Merge pull request #195 from subwaystation/dev

6719020

bump to 1.2.0dev

update workflow svg

1708db9

finished makeup2

411a5dc

Merge pull request #199 from nf-core/workflow_svg

1aed918

update workflow svg

Template update for nf-core/tools version 2.14.0

cdc1494

Template update for nf-core/tools version 2.14.1

1e52981

Template update for nf-core/tools version 3.0.0

d4a3def

Template update for nf-core/tools version 3.0.1

f21fb92

Template update for nf-core/tools version 3.0.2

e7671c6

Template update for nf-core/tools version 3.1.0

62f8366

Template update for nf-core/tools version 3.1.1

782e1c6

Merged changes from nf-core template

67b3acf

Fix up invalid input values

a6622ad

Fix up incorrectly typed input values

407820f

Add exceptions to files_exist lint check

3c96fea

Removing unnecessary fastqc test files

62bf0eb

Remove samplesheet output channel from PIPELINE_INITIALIZATION

3ffab69

Update to nf-core/setup-nextflow@2 in custom CI jobs

6d2b02f

Add missing ch_versions channel

57aee62

Fix up pangenome workflow

973bbe9

Attempt to fix lint errors

a67f17e

Set validation lenientMode to true

f038844

Address review comments

0947d1f

Merge pull request #213 from heuermh/merging-template-updates

5a5941c

Merging template updates for versions 2.14.0 through 3.1.1

Update nf-core/smoothxg module to version 0.8.0

784a9af

Merge pull request #216 from heuermh/smoothxg-0.8.0

10beeb4

Update nf-core/smoothxg module to version 0.8.0

make n_haplotypes null

1d128e7

Merge pull request #220 from nf-core/i218

b1bca81

make parameter `n_haplotypes` null

Refactor authors to list of contributors

8fd5000

heuermh and others added 20 commits January 23, 2025 09:54

Merge branch 'multiqc_community_1.25' of https://github.com/nf-core/p…

1471964

…angenome into odgi-0.9.0

update pggb docker to contain vg v1.62

2e9a283

Template update for nf-core/tools version 3.2.0

abe9a5f

Apply suggestions from code review

c8a7f9a

Co-authored-by: Friederike Hanssen <[email protected]>

Apply suggestions from code review

f0d2287

Merge pull request #234 from nf-core/vg_1.62

d5156bd

update pggb docker to contain vg v1.62

Attempt to fix prettier lint error

c9a6ec3

Attempt to fix prettier lint error

312e13c

Merge pull request #222 from heuermh/contributors

f5fb5a8

Refactor authors to list of contributors

Merge branch 'dev' of https://github.com/nf-core/pangenome into odgi-…

42671dd

…0.9.0

Update multiqc_community to version 1.26

76654ad

fix odgi stats table not appearing

08e0e73

Merge pull request #233 from heuermh/odgi-0.9.0

d22b333

Update nf-core odgi modules to version 0.9.0

resolve merge conflicts, local multiqc to v1.27

ff2e8c1

Merge pull request #235 from nf-core/nf-core-template-merge-3.2.0

cdb5f70

Important! Template update for nf-core/tools v3.2.0

prepare 1.1.3 release

38c1d9a

commit hidden file

5558242

prettier

6e611e8

Merge pull request #236 from subwaystation/dev

7c435e5

prepare new release 1.1.3 - marsupial

Resolve merge conflicts

63b639b

Merge pull request #238 from heuermh/dev

d292756

Resolve merge conflicts

heuermh added 2 commits January 30, 2025 16:31

Fix release lint error

ae0ff02

Retrigger CI checks

40c25e8

Merge pull request #239 from heuermh/1.1.3-release-lint

1fcf24e

Fix 1.1.3 release lint error(s)

Provide feedback

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Release version 1.1.3 #237

Release version 1.1.3 #237

heuermh commented Jan 30, 2025

heuermh commented Jan 30, 2025

github-actions bot commented Jan 30, 2025 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

subwaystation commented Jan 30, 2025

heuermh commented Jan 31, 2025

heuermh commented Jan 31, 2025

subwaystation commented Jan 31, 2025

Release version 1.1.3 #237

Are you sure you want to change the base?

Release version 1.1.3 #237

Conversation

heuermh commented Jan 30, 2025

PR checklist

heuermh commented Jan 30, 2025

github-actions bot commented Jan 30, 2025 • edited Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

subwaystation commented Jan 30, 2025

heuermh commented Jan 31, 2025

heuermh commented Jan 31, 2025

subwaystation commented Jan 31, 2025

github-actions bot commented Jan 30, 2025 •

edited

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