v1.0.0 #66

BarryDigby · 2022-12-13T10:39:03Z

DSL2 version of nf-core/circrna.

A few minor comments on the linting warnings:

I need some assistance configuring the full AWS test dataset. The data can be accessed via SRA, this should be straightforward using fetchngs.
Links to manuscripts / DOI links - I have a paper for the workflow currently under review, I'm hoping this will be accepted soon having addressed reviewer comments.

github-actions · 2023-02-01T10:53:05Z

Python linting (`black`) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

Install black: pip install black
Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

maxulysse · 2023-10-27T11:36:40Z

I feel like comments from #69 haven't been integrated in this PR yet.

github-actions · 2024-02-02T08:53:57Z

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

Posted for pipeline commit 98923dd

+| ✅ 216 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).

✅ 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-circrna_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-circrna_logo_light.png
files_exist - File found: docs/images/nf-core-circrna_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 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-circrna_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/WorkflowCircrna.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 - 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: dev
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.tool= circexplorer2
nextflow_config - Config default value correct: params.bsj_reads= 0
nextflow_config - Config default value correct: params.tool_filter= 0
nextflow_config - Config default value correct: params.duplicates_fun= mean
nextflow_config - Config default value correct: params.save_intermediates= false
nextflow_config - Config default value correct: params.exon_boundary= 200
nextflow_config - Config default value correct: params.sjdboverhang= 100
nextflow_config - Config default value correct: params.chimJunctionOverhangMin= 10
nextflow_config - Config default value correct: params.alignSJDBoverhangMin= 10
nextflow_config - Config default value correct: params.limitSjdbInsertNsj= 1000000
nextflow_config - Config default value correct: params.chimSegmentMin= 10
nextflow_config - Config default value correct: params.seglen= 25
nextflow_config - Config default value correct: params.min_intron= 20
nextflow_config - Config default value correct: params.max_intron= 1000000
nextflow_config - Config default value correct: params.min_map_len= 40
nextflow_config - Config default value correct: params.min_fusion_distance= 200
nextflow_config - Config default value correct: params.bootstrap_samples= 30
nextflow_config - Config default value correct: params.save_unaligned= false
nextflow_config - Config default value correct: params.save_reference= true
nextflow_config - Config default value correct: params.hisat2_build_memory= 200.GB
nextflow_config - Config default value correct: params.skip_trimming= false
nextflow_config - Config default value correct: params.save_trimmed= false
nextflow_config - Config default value correct: params.skip_fastqc= false
nextflow_config - Config default value correct: params.min_trimmed_reads= 10000
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= 50
nextflow_config - Config default value correct: params.max_memory= 300.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
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-circrna_logo_light.png matches the template
files_unchanged - docs/images/nf-core-circrna_logo_light.png matches the template
files_unchanged - docs/images/nf-core-circrna_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: 23.04.0, Config: 23.04.0
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (382 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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.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 - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
modules_config - CLEAN_FASTA found in conf/modules.config and Nextflow scripts.
modules_config - SEQKIT_SPLIT found in conf/modules.config and Nextflow scripts.
modules_config - BOWTIE_BUILD found in conf/modules.config and Nextflow scripts.
modules_config - BOWTIE2_BUILD found in conf/modules.config and Nextflow scripts.
modules_config - BWA_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - HISAT2_EXTRACTSPLICESITES found in conf/modules.config and Nextflow scripts.
modules_config - HISAT2_BUILD found in conf/modules.config and Nextflow scripts.
modules_config - STAR_GENOMEGENERATE found in conf/modules.config and Nextflow scripts.
modules_config - FILTER_BSJS found in conf/modules.config and Nextflow scripts.
modules_config - UPSET_SAMPLES found in conf/modules.config and Nextflow scripts.
modules_config - UPSET_ALL found in conf/modules.config and Nextflow scripts.
modules_config - ADD_BACKSPLICE found in conf/modules.config and Nextflow scripts.
modules_config - COMBINE_TRANSCRIPTOME_GTFS found in conf/modules.config and Nextflow scripts.
modules_config - EXCLUDE_OVERLONG_TRANSCRIPTS found in conf/modules.config and Nextflow scripts.
modules_config - MARK_CIRCULAR found in conf/modules.config and Nextflow scripts.
modules_config - TARGETSCAN_DATABASE found in conf/modules.config and Nextflow scripts.
modules_config - TARGETSCAN found in conf/modules.config and Nextflow scripts.
modules_config - MIRANDA found in conf/modules.config and Nextflow scripts.
modules_config - MIRNA_TARGETS 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: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-06-19 19:30:35

Add filter for circular RNAs to find_circ

Implement ciriquant quantification

Add parameter for grouping detected circRNAs that are very close

Versioning

Important! Template update for nf-core/tools v3.0.2

BarryDigby mentioned this pull request Dec 22, 2022

Important! Template update for nf-core/tools v2.7.2 #67

Closed

jfy133 assigned jfy133 and FriederikeHanssen Jan 19, 2023

jfy133 mentioned this pull request Jan 23, 2023

[Do not merge!] Pseudo PR for first release #69

Draft

nictru and others added 23 commits August 1, 2024 10:57

Update comment

3be2733

Merge pull request #165 from nf-core/find_circ_bug

eb025f6

Add filter for circular RNAs to find_circ

Add error message for empty intersections

a66fcd3

Add docs for GTF required attributes

02a19f2

Add check for presence of attributes in annotation intersection

2e3d667

Fix bug in missing attribute check

3a8e88c

Implement Segemehl grouping

b008653

Add bedtools groupby

9d79972

Fix segemehl grouping

50a1817

Implement ordering of segemehl results

9fc67a1

Implement check for duplicates in tool results

08d56cc

Implement custom BSJome generation

7d470e6

Extract annotation from discovery

8719a3f

Fix bug in tool filtering

8509cb0

Fix saveAs conditions

d26712e

Fix some output definitions

b45cea8

Add per-sample and combined output directories for discovery

11892e2

Add tools subdirectory to discovery outdir

a0f3e73

Implement separate processes for FASTA extraction

ea4ef34

Add fastas to discovery output

8e7e441

Add output directory for statistical tests

4e9f4ab

Handle output of circtest_prepare

4e2ce6c

Improve QC output directory structure

ca5e4b6

nictru and others added 30 commits September 26, 2024 10:51

Fix outdir definition

7f291d6

Merge pull request #172 from nf-core/ciriquant

edced9e

Implement ciriquant quantification

Merge upset plotting with sample combine_beds

866b525

Change the way combine_bed is parametrized

ceb8211

Fix empty checks

2dfdb09

Improve error message on empty

0b3529c

Prettier

df4966c

Editorconfig

3311825

Remove upset process configs

0586ec2

Make combine_beds plot outputs optional

44caaf3

Merge pull request #173 from nf-core/microshifts

f96729c

Add parameter for grouping detected circRNAs that are very close

Fix version numbering

dc2edf1

Add nico as an author

f0ab465

Init changelog

50dc307

Fill "added" field in Changelog

a634d32

Fix http json schema URLs

cc6bff6

Prettier

7b3dd3a

Merge pull request #174 from nf-core/versioning

050d0b2

Versioning

Template update for nf-core/tools version 3.0.2

8f1c8f8

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

da8077c

Remove nf-validation trace

9cf7487

Update nextflow required version badge

1df9e74

Restructure some param locations to comply with latest schema

fb2b920

Update testdata base path references

f01f1b2

Fix test dataset base path usage

b9c3868

Update json schema

3d2f46a

Fix multiQC call

f92eabb

Fix channel structure bug

1b6028c

Remove old way of specifying resource limits

aa4a104

Merge pull request #175 from nf-core/nf-core-template-merge-3.0.2

849da6a

Important! Template update for nf-core/tools v3.0.2

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

v1.0.0 #66

v1.0.0 #66

BarryDigby commented Dec 13, 2022

github-actions bot commented Feb 1, 2023

maxulysse commented Oct 27, 2023

github-actions bot commented Feb 2, 2024 •

edited

Loading

❗ Test warnings:

✅ Tests passed:

Run details

v1.0.0 #66

Are you sure you want to change the base?

v1.0.0 #66

Conversation

BarryDigby commented Dec 13, 2022

github-actions bot commented Feb 1, 2023

Python linting (black) is failing

maxulysse commented Oct 27, 2023

github-actions bot commented Feb 2, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

Python linting (`black`) is failing

github-actions bot commented Feb 2, 2024 •

edited

Loading

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