release 1.1.0 - Schmuddlweddr #179

subwaystation · 2024-02-27T12:36:19Z

PR checklist

Update from Master to add DOI

Update modules gfaffix, MultiQC, samtools/faidx

Update `vg deconstruct` to v1.50.1

update smoothxg to v0.7.1

also put DRAW into MultiQC report

another MultiQC fix

Update modules odgi and wfmash

Important! Template update for nf-core/tools v2.13

prepare 1.1.0 release - Schmuddlweddr

github-actions · 2024-02-27T12:37:46Z

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

Posted for pipeline commit d51fa7a

+| ✅ 186 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
nextflow_config - Config manifest.version should end in dev: 1.1.0
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
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_unchanged - File ignored due to lint config: assets/nf-core-pangenome_logo_light.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: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: .nf-core.yaml
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: .github/workflows/push_dockerhub.yml
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: docs/images/nf-core-pangenome_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
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/Workflow.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/WorkflowPangenome.groovy
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.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.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.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.validationLenientMode= true
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/images/nf-core-pangenome_logo_light.png matches the template
files_unchanged - docs/images/nf-core-pangenome_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
files_unchanged - pyproject.toml 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
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (175 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: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: ci.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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.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' 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'

Run details

nf-core/tools version 2.13
Run at 2024-02-28 09:15:28

CHANGELOG.md

nextflow_schema.json

CHANGELOG.md

assets/schema_input.json

modules/local/paf2net/main.nf

nextflow_schema.json

subworkflows/local/utils_nfcore_pangenome_pipeline/main.nf

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Some fixes for the release

subwaystation · 2024-02-27T14:09:50Z

Alright, I think I addressed everything @mashehu. Thanks for the detailed feedback :)

heuermh

LGTM, very minor changes requested, and one question about the DOI in the terminal output.

Test runs succeed for me, tested with Docker on EC2 linux and osx

$ nextflow run main.nf -profile docker,test --outdir test-results
N E X T F L O W  ~  version 23.04.3
Launching `main.nf` [soggy_davinci] DSL2 - revision: a4c3964401
Downloading plugin [email protected]
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/pangenome v1.1.0
------------------------------------------------------
...
[4d/27b1c4] process > NFCORE_PANGENOME:PANGENOME:MULTIQC                                                               [100%] 1 of 1 ✔
-[nf-core/pangenome] Pipeline completed successfully-
Completed at: 27-Feb-2024 11:42:47
Duration    : 2m 46s
CPU hours   : (a few seconds)
Succeeded   : 22

workflows/pangenome.nf

subworkflows/local/pggb.nf

subworkflows/local/odgi_qc.nf

nextflow_schema.json

subwaystation · 2024-02-28T09:15:33Z

Thanks @heuermh! If you are happy now, please approve ;)

heuermh · 2024-02-28T13:12:18Z

Very happy, thank you! 😁

subwaystation added 30 commits June 21, 2023 14:20

update samtools faidx moduels

e11b3de

bump to 1.1.0dev

89f0b14

try manual fix of multiqc_config

48d6a3a

Merge branch 'dev' into doi

dfa05a6

Merge pull request #137 from nf-core/doi

3cc66d8

Update from Master to add DOI

update gfaffix, multiqc, samtools/faidx

5375a6b

try to fix samtools/faidx

c28f08d

Merge pull request #145 from nf-core/update/modules

818f809

Update modules gfaffix, MultiQC, samtools/faidx

vg deconstruct 1.50.1

1651210

Merge branch 'dev' into update/modules

ffb263e

Merge pull request #146 from nf-core/update/modules

3053320

Update `vg deconstruct` to v1.50.1

update smoothxg to v0.7.1

63707cb

Merge pull request #147 from nf-core/update/modules

cefbdde

update smoothxg to v0.7.1

also put DRAW into MultiQC report

d1f0eec

Merge pull request #148 from nf-core/fix/multiqc

c06ddc5

also put DRAW into MultiQC report

another MultiQC fix

f69a7f9

life is strange

9eafdf3

Merge pull request #149 from nf-core/fix/multiqc

b2cd62d

another MultiQC fix

Merge branch 'dev' into update_modules

27e851d

update odgi and wfmash

1b545e9

Merge pull request #150 from nf-core/update_modules

b70ace7

Update modules odgi and wfmash

fix wfmash_sparse_map parameter

a1f8072

add wfmash_sparse_map test

16bcbcc

try linter fix

6538720

try fix

dc5495a

add wfmash_sparse_map to ignored params

2904385

revert to string theory

2570fd5

remove ignore parameter --wfmash_sparse_map

a2a4fe4

update tests, add pattern

7575ba1

update CI, fix linting error

90ebc5d

subwaystation added 6 commits February 27, 2024 10:56

bug fix

5f2c926

remove customdumpsoftwareversions

d2c276b

hopefully final conflict resolved

c038675

Merge pull request #171 from nf-core/nf-core-template-merge-2.13

e1f188b

Important! Template update for nf-core/tools v2.13

prepare 1.1.0 release

f3a2da6

Merge pull request #178 from subwaystation/dev

b1f5f16

prepare 1.1.0 release - Schmuddlweddr

subwaystation requested a review from heuermh February 27, 2024 12:42

mashehu requested changes Feb 27, 2024

View reviewed changes

subwaystation and others added 11 commits February 27, 2024 14:02

Update CHANGELOG.md

0627dcd

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Update CHANGELOG.md

3a99032

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Update nextflow_schema.json

bc1f113

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Update CHANGELOG.md

6db3921

Co-authored-by: Matthias Hörtenhuber <[email protected]>

more detailed wfmash_hg_filter_ani_diff explanation

2a659ee

description for wfmash_hg_filter_ani_diff

e91f751

Merge pull request #180 from subwaystation/dev

b9ce7c5

Some fixes for the release

delete assets/schema_input.json

b986c4a

update toolCitationText()

8d35f15

better help text for wfmash_exclude_delim

4fafe05

update toolBibliographyText()

2876894

mashehu approved these changes Feb 27, 2024

View reviewed changes

heuermh requested changes Feb 27, 2024

View reviewed changes

workflows/pangenome.nf Show resolved Hide resolved

subworkflows/local/pggb.nf Outdated Show resolved Hide resolved

subworkflows/local/odgi_qc.nf Outdated Show resolved Hide resolved

nextflow_schema.json Outdated Show resolved Hide resolved

subwaystation added 3 commits February 28, 2024 10:05

proper doi for the pipeline

203c65f

fix typos

02725ae

tell users that in the future the PanSN spec will be mandatory

d51fa7a

heuermh approved these changes Feb 28, 2024

View reviewed changes

subwaystation merged commit 9740ffc into master Feb 28, 2024
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release 1.1.0 - Schmuddlweddr #179

release 1.1.0 - Schmuddlweddr #179

subwaystation commented Feb 27, 2024 •

edited

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github-actions bot commented Feb 27, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

subwaystation commented Feb 27, 2024

heuermh left a comment

subwaystation commented Feb 28, 2024

heuermh commented Feb 28, 2024

release 1.1.0 - Schmuddlweddr #179

release 1.1.0 - Schmuddlweddr #179

Conversation

subwaystation commented Feb 27, 2024 • edited Loading

PR checklist

github-actions bot commented Feb 27, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

subwaystation commented Feb 27, 2024

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subwaystation commented Feb 28, 2024

heuermh commented Feb 28, 2024

subwaystation commented Feb 27, 2024 •

edited

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github-actions bot commented Feb 27, 2024 •

edited

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