Seqkit #58

sarahjeeeze · 2024-10-29T14:32:35Z

Added seqkit stats module to the workflow - looking for review

PR checklist

Issue with the previous implementation was that sometimes MULTIQC_PER_LANE would execute before the extra files were collected into `ch_multiqc_extra_files`, causing `null` to be added to the list of files passed to multiqc.

Important! Template update for nf-core/tools v2.14.1

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

…uts w. empty channels

Some additions

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

Implement tagging system

Manual merge nf-core-tools 3.0.2

sarahjeeeze · 2024-10-29T14:34:05Z

ah meant to do it in to dev will try again

github-actions · 2024-10-29T14:34:51Z

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 @sarahjeeeze,

It looks like this pull-request is has been made against the nf-core/seqinspector 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/seqinspector 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 · 2024-10-29T14:39:37Z

`nf-core pipelines lint` overall result: Failed ❌

Posted for pipeline commit d806380

+| ✅ 190 tests passed       |+
!| ❗  21 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

included_configs - Pipeline config does not include custom configs. Please uncomment the includeConfig line.

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
pipeline_todos - TODO string in README.md: TODO nf-core:
pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
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!
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

✅ 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-seqinspector_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-seqinspector_logo_light.png
files_exist - File found: docs/images/nf-core-seqinspector_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: conf/igenomes_ignored.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 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-seqinspector_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/WorkflowSeqinspector.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: 3.0.2
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.igenomes_base= s3://ngi-igenomes/igenomes/
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/
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-seqinspector_logo_light.png matches the template
files_unchanged - docs/images/nf-core-seqinspector_logo_light.png matches the template
files_unchanged - docs/images/nf-core-seqinspector_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
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
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/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.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
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'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - SEQKIT_STATS found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC_GLOBAL found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC_PER_TAG 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: 3.0.2
version_consistency - Version tags are numeric and consistent between container, release tag and config.

Run details

nf-core/tools version 3.0.2
Run at 2024-10-29 14:34:53

Aratz and others added 30 commits March 28, 2024 16:14

Generate reports per lane, group and rundir

a31040e

Improve formatting

0da5870

Improve output sorting

d233d8f

Use group instead of project

307e43c

Fix output channel

627cf94

Fix linting

c9ba028

Give credits back to NGI

2cfc91d

Fix file names

fbfb02d

Set up tests

8a19929

point test conf upstream

eba628e

project -> group

23f69d1

project -> group

1ebf3f1

make lane non-compulsory

b0bf471

remove unused file

9e0eca3

revamp nf-test, run once for each sequencing platform

98e60bf

Update modules and subworkflows

d95c660

Fix multiqc extra files

e0527cc

Issue with the previous implementation was that sometimes MULTIQC_PER_LANE would execute before the extra files were collected into `ch_multiqc_extra_files`, causing `null` to be added to the list of files passed to multiqc.

Template update for nf-core/tools version 2.14.0

93c66a4

Template update for nf-core/tools version 2.14.1

88ca813

Merge branch 'dev' into nf-core-template-merge-2.14.1

ba72067

Add test snapshots

42159a1

Remove unused module configuration

ef61f9f

Update usage docs and restore example samplesheet

51b01e9

Update output docs

7c7f31f

Update changelog

1c4f6e0

Update samplesheet in readme file

211bfaf

Merge pull request #15 from nf-core/nf-core-template-merge-2.14.1

e93baf9

Important! Template update for nf-core/tools v2.14.1

Merge remote-tracking branch 'origin/dev' into multiqc_multireport

acc82d0

Run prettier

df4e9cb

Use testdata base path param in tests/MiSeq.main.nf.test

2303db9

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

kedhammar and others added 26 commits August 27, 2024 15:52

Try adding regex assertion and error for samplesheet tags

8bba888

Add missing comma

6987e93

Change example tags to more neutral ones

363e782

Check for tag collisions

c1a21de

Use columns to separate tags

8a43efa

switch to colon-separated tags

8779909

use testdata with tags

f496b85

Make ids unique

38e39a9

bump multiqc to prevent gitpod crashing, populate the new process inp…

c96a41c

…uts w. empty channels

Merge branch 'dev' into dev

49484f3

Merge pull request #1 from kedhammar/dev

1c364d3

Some additions

Allow for uppercase letters

2e269ec

Use samplesheet row in id

c97a597

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

Update snapshots

1f33928

Merge pull request #20 from Aratz/dev

5bea1e5

Implement tagging system

Template update for nf-core/tools version 3.0.0

f530e31

Template update for nf-core/tools version 3.0.1

d5d1a04

Template update for nf-core/tools version 3.0.2

7566c9f

nf-core tools 3.0.2 modules update

7ce086a

Merge branch 'nf-core-template-merge-3.0.2' into merge-template-3.0.2

4918a25

merge fix

a595130

update snapshots

0364088

Update CHANGELOG.md

545af04

Merge pull request #49 from nf-core/merge-template-3.0.2

30f2306

Manual merge nf-core-tools 3.0.2

add seqkit module

dad5d6d

seqkit

d806380

sarahjeeeze closed this Oct 29, 2024

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Seqkit #58

Seqkit #58

sarahjeeeze commented Oct 29, 2024

sarahjeeeze commented Oct 29, 2024

github-actions bot commented Oct 29, 2024

github-actions bot commented Oct 29, 2024 •

edited

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❌ Test failures:

❗ Test warnings:

✅ Tests passed:

Run details

Seqkit #58

Seqkit #58

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sarahjeeeze commented Oct 29, 2024

PR checklist

sarahjeeeze commented Oct 29, 2024

github-actions bot commented Oct 29, 2024

This PR is against the master branch ❌

github-actions bot commented Oct 29, 2024 • edited Loading

nf-core pipelines lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

✅ Tests passed:

Run details

This PR is against the `master` branch ❌

github-actions bot commented Oct 29, 2024 •

edited

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`nf-core pipelines lint` overall result: Failed ❌