Correcting the NANOPORE and FASTA reads channel #457

LilyAnderssonLee · 2024-03-18T09:56:32Z

PR checklist

Sync with dev

This reverts commit 1a37251.

Co-authored-by: Lili Andersson-Li <[email protected]>

Add nonpareil

Co-authored-by: James A. Fellows Yates <[email protected]>

Bump up the pipeline version number in the dev branch

Dev to bouncy-basenji

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

… path and directory

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

remove commented code about unique db_name check

Replace the db_params:null into empty string "".

Add meta.single_end to ch_input.nanopore channel

…13.1 Important! Template update for nf-core/tools v2.13.1

Merge dev into bouncy-basenji

github-actions · 2024-03-18T09:56:45Z

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 @LilyAnderssonLee,

It looks like this pull-request is has been made against the LilyAnderssonLee/taxprofiler 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 LilyAnderssonLee/taxprofiler 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!

LilyAnderssonLee · 2024-03-18T09:57:19Z

Close it, should merge into bouncy-basenji branch

github-actions · 2024-03-18T09:58:37Z

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

Posted for pipeline commit 9373a96

+| ✅ 194 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

✅ 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-taxprofiler_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-taxprofiler_logo_light.png
files_exist - File found: docs/images/nf-core-taxprofiler_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: conf/igenomes.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-taxprofiler_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/WorkflowTaxprofiler.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: 1.1.6dev
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.preprocessing_qc_tool= fastqc
nextflow_config - Config default value correct: params.shortread_qc_tool= fastp
nextflow_config - Config default value correct: params.shortread_qc_minlength= 15
nextflow_config - Config default value correct: params.shortread_complexityfilter_tool= bbduk
nextflow_config - Config default value correct: params.shortread_complexityfilter_entropy= 0.3
nextflow_config - Config default value correct: params.shortread_complexityfilter_bbduk_windowsize= 50
nextflow_config - Config default value correct: params.shortread_complexityfilter_fastp_threshold= 30
nextflow_config - Config default value correct: params.shortread_complexityfilter_prinseqplusplus_mode= entropy
nextflow_config - Config default value correct: params.shortread_complexityfilter_prinseqplusplus_dustscore= 0.5
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_minlength= 1000
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_keeppercent= 90
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_targetbases= 500000000
nextflow_config - Config default value correct: params.shortread_redundancyestimation_mode= kmer
nextflow_config - Config default value correct: params.diamond_output_format= tsv
nextflow_config - Config default value correct: params.kaiju_taxon_rank= species
nextflow_config - Config default value correct: params.krakenuniq_ram_chunk_size= 16G
nextflow_config - Config default value correct: params.krakenuniq_batch_size= 20
nextflow_config - Config default value correct: params.malt_mode= BlastN
nextflow_config - Config default value correct: params.kmcp_mode= 3
nextflow_config - Config default value correct: params.ganon_report_type= reads
nextflow_config - Config default value correct: params.ganon_report_toppercentile= 0
nextflow_config - Config default value correct: params.ganon_report_mincount= 0
nextflow_config - Config default value correct: params.ganon_report_maxcount= 0
nextflow_config - Config default value correct: params.standardisation_taxpasta_format= tsv
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.igenomes_base= s3://ngi-igenomes/igenomes/
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 - assets/nf-core-taxprofiler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-taxprofiler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-taxprofiler_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
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (283 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: awstest.yml
actions_schema_validation - Workflow validation passed: fix-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: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting.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 2.13.1
Run at 2024-03-18 09:58:17

jfy133 and others added 30 commits November 9, 2023 19:57

Install module

a58388c

Merge pull request nf-core#416 from nf-core/dev

b25350c

Sync with dev

Add get it working, add to tests, update docs/images/citations

69e0d09

Fix groovy semantic errors

2c24711

update gitignore to ignore nf-test

1a37251

Revert "update gitignore to ignore nf-test"

240634c

This reverts commit 1a37251.

Fix nonpareil args across all tests

5e853b0

Add nonpareil

a050658

Minor linting

ff16394

Fix channel emission

46bf2b2

Fix module linting

c69b00e

Add nonpareil to valid MultiQC entries

a0d5821

Final linting

c1d12d9

[automated] Fix linting with Prettier

88b8e1a

Apply suggestions from code review

40d1bfa

Co-authored-by: Lili Andersson-Li <[email protected]>

Merge pull request nf-core#417 from nf-core/add-nonpareil

ffff2e6

Add nonpareil

Merge branch 'dev' into bouncy-basenji

5ea76e8

Merge dev into bouncy-basenji

f4dd39b

Fix prettier

f00bd54

Remove merge marker

45dd3c9

Apply review suggestions

c2a15e2

Merge branch 'nf-core:dev' into dev

444d323

Bump to new dev version

154a219

Prettier

e04e613

Update CHANGELOG.md

7a86d96

Co-authored-by: James A. Fellows Yates <[email protected]>

Merge pull request nf-core#447 from genomic-medicine-sweden/bump_version

32a5539

Bump up the pipeline version number in the dev branch

Merge branch 'bouncy-basenji' into fix-merge-conflict

d9de044

Merge pull request nf-core#448 from nf-core/fix-merge-conflict

aa6d088

Dev to bouncy-basenji

Template update for nf-core/tools version 2.13

1041602

Template update for nf-core/tools version 2.13.1

53439cb

LilyAnderssonLee and others added 18 commits March 1, 2024 14:46

update the template and add nf-validation

b12a0bd

remove custom_dumpsoftwareversions

0310d75

Update .github/workflows/ci.yml

1c515f5

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

Update ci.yml

d5e6133

update error message in schema_databases.json

132a734

Update the db_path format definition to include both options for file…

5516e87

… path and directory

Update main.nf

7f9d873

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

Update assets/schema_database.json

af065d8

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

Update assets/schema_database.json

9389c31

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

Update assets/schema_database.json

596708b

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

update db_params in schema_databases.json

b730faa

Update taxprofiler.nf

c1e09b5

remove commented code about unique db_name check

Update taxprofiler.nf

bfe9aa8

Replace the db_params:null into empty string "".

Update taxprofiler.nf

54640ea

Add meta.single_end to ch_input.nanopore channel

Merge pull request nf-core#454 from nf-core/nf-core-template-merge-2.…

e81f171

…13.1 Important! Template update for nf-core/tools v2.13.1

Merge dev into bouncy-basenji

c22f6e9

Merge pull request nf-core#455 from LilyAnderssonLee/bouncy-basenji

faf93e9

Merge dev into bouncy-basenji

update the nanopore and fasta input channel

9373a96

LilyAnderssonLee closed this Mar 18, 2024

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Correcting the NANOPORE and FASTA reads channel #457

Correcting the NANOPORE and FASTA reads channel #457

LilyAnderssonLee commented Mar 18, 2024

github-actions bot commented Mar 18, 2024

LilyAnderssonLee commented Mar 18, 2024

github-actions bot commented Mar 18, 2024

❗ Test warnings:

✅ Tests passed:

Run details

Correcting the NANOPORE and FASTA reads channel #457

Correcting the NANOPORE and FASTA reads channel #457

Conversation

LilyAnderssonLee commented Mar 18, 2024

PR checklist

github-actions bot commented Mar 18, 2024

This PR is against the master branch ❌

LilyAnderssonLee commented Mar 18, 2024

github-actions bot commented Mar 18, 2024

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

This PR is against the `master` branch ❌

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