Fix wfmash exclude delim #169

subwaystation · 2024-02-20T15:09:38Z

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

make the use of chunks explicit

…-2.12

Important! Template update for nf-core/tools v2.12

update modules

Put functions within closure to evaluate them properly.

update wfmash, multiqc

github-actions · 2024-02-20T15:09:51Z

This PR is against the `master` branch ❌

Do not close this PR
Click Edit and change the base to dev
This CI test will remain failed until you push a new commit

Hi @subwaystation,

It looks like this pull-request is has been made against the nf-core/pangenome master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/pangenome dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

github-actions · 2024-02-20T15:11:19Z

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

Posted for pipeline commit fe5c1c9

+| ✅ 186 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
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 WorkflowPangenome.groovy: Optionally add in-text citation tools to this list.

❔ 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: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
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: lib/WorkflowPangenome.groovy
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/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 manifest.version ends in dev: 1.1.0dev
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.seqwish_min_match_length= 19
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.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 - lib/NfcoreTemplate.groovy 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 (163 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 2.12.1
Run at 2024-02-20 15:10:48

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 and others added 26 commits October 31, 2023 10:15

Merge pull request #160 from nf-core/wfmash_power_up

db11552

make the use of chunks explicit

Template update for nf-core/tools version 2.11

03af9b1

Template update for nf-core/tools version 2.11.1

49207d8

Template update for nf-core/tools version 2.12

3f309cc

Merge remote-tracking branch 'origin/dev' into nf-core-template-merge…

f129661

…-2.12

prettier, but not pretty enough

87abe94

maybe happy

86cdd25

fix linter

fee6eb0

DE(A)VD container

905e176

fix most linting errors

0191e18

oh be pretty, oh be smart: don't start

564c039

Merge pull request #163 from nf-core/nf-core-template-merge-2.12

79ea215

Important! Template update for nf-core/tools v2.12

update modules

a8f4b2b

revert wfmash to 0.10.5

ef49965

now

a78db05

Merge pull request #164 from nf-core/update_modules

8e2eed3

update modules

update wfmash, multiqc

c621412

bug fix

59b0113

another try

e41a525

another wfmash update

c873b10

another wfmash update

e3bd04c

Put functions within closure to evaluate them properly.

28e73b1

Merge pull request #166 from nf-core/config_function_fix

1d2915b

Put functions within closure to evaluate them properly.

Merge branch 'dev' into update_modules

6914080

Merge pull request #165 from nf-core/update_modules

c8cad90

update wfmash, multiqc

fix delim bug

fe5c1c9

subwaystation closed this Feb 20, 2024

heuermh deleted the fix_wfmash_exclude_delim branch February 22, 2024 16:14

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Fix wfmash exclude delim #169

Fix wfmash exclude delim #169

subwaystation commented Feb 20, 2024

github-actions bot commented Feb 20, 2024

github-actions bot commented Feb 20, 2024

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Fix wfmash exclude delim #169

Fix wfmash exclude delim #169

Conversation

subwaystation commented Feb 20, 2024

PR checklist

github-actions bot commented Feb 20, 2024

This PR is against the master branch ❌

github-actions bot commented Feb 20, 2024

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

This PR is against the `master` branch ❌

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