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 👍

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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 pipelines lint` overall result: Failed ❌

Posted for pipeline commit abdc4cb

+| ✅ 265 tests passed       |+
!| ❗   9 tests had warnings |!
-| ❌   3 tests failed       |-

❌ Test failures:

nextflow_config - Config manifest.version should not contain dev for a release: 0.0.1dev
version_consistency - manifest.version was not numeric: 0.0.1dev!
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 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: 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 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 base.config: Check the defaults for all 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-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: 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-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 - 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 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.tools= circexplorer2
nextflow_config - Config default value correct: params.bsj_reads= 1
nextflow_config - Config default value correct: params.max_shift= 0
nextflow_config - Config default value correct: params.consider_strand= true
nextflow_config - Config default value correct: params.min_tools= 1
nextflow_config - Config default value correct: params.min_samples= 1
nextflow_config - Config default value correct: params.quantification_tools= ciriquant,psirc,sum,max
nextflow_config - Config default value correct: params.bootstrap_samples= 30
nextflow_config - Config default value correct: params.mirna_min_sample_percentage= 0.2
nextflow_config - Config default value correct: params.mirna_min_reads= 5
nextflow_config - Config default value correct: params.mirna_correlation= pearson
nextflow_config - Config default value correct: params.mirna_tools= miranda,targetscan
nextflow_config - Config default value correct: params.mirna_min_tools= 1
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.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.igenomes_base= s3://ngi-igenomes/igenomes/
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.save_intermediates= false
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-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: 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 - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTQ found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
modules_config - CLEAN_FASTA found in conf/modules.config and Nextflow scripts.
modules_config - GTFFILTER 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 - EXTRACT_COUNTS found in conf/modules.config and Nextflow scripts.
modules_config - COMBINE_COUNTS_PER_TOOL found in conf/modules.config and Nextflow scripts.
modules_config - BED_ADD_SAMPLE_TOOL found in conf/modules.config and Nextflow scripts.
modules_config - COMBINE_TOOLS_PER_SAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - COMBINE_SAMPLES found in conf/modules.config and Nextflow scripts.
modules_config - FASTA_COMBINED found in conf/modules.config and Nextflow scripts.
modules_config - FASTA_PER_SAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - FASTA_PER_SAMPLE_TOOL found in conf/modules.config and Nextflow scripts.
modules_config - ADD_INTRONS found in conf/modules.config and Nextflow scripts.
modules_config - EXTRACT_EXONS_INTRONS found in conf/modules.config and Nextflow scripts.
modules_config - ADD_BACKSPLICE found in conf/modules.config and Nextflow scripts.
modules_config - UNIFY_MIRANDA found in conf/modules.config and Nextflow scripts.
modules_config - UNIFY_TARGETSCAN found in conf/modules.config and Nextflow scripts.
modules_config - COMBINE_BINDINGSITES 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 - TRANSCRIPTOME found in conf/modules.config and Nextflow scripts.
modules_config - MARK_CIRCULAR found in conf/modules.config and Nextflow scripts.
modules_config - PSIRC_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - RUN_PSIRC_QUANT found in conf/modules.config and Nextflow scripts.
modules_config - CUSTOM_TX2GENE found in conf/modules.config and Nextflow scripts.
modules_config - TXIMETA_TXIMETA found in conf/modules.config and Nextflow scripts.
modules_config - TXIMETA_TXIMPORT found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_EXPERIMENTS 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.
modules_config - COMBINE_BINDINGSITES found in conf/modules.config and Nextflow scripts.
modules_config - MAJORITY_VOTE found in conf/modules.config and Nextflow scripts.
modules_config - CIRCTEST_PREPARE found in conf/modules.config and Nextflow scripts.
modules_config - CIRCTEST_CIRCTEST found in conf/modules.config and Nextflow scripts.
modules_config - CIRIQUANT_PREPDE found in conf/modules.config and Nextflow scripts.
modules_config - STRINGTIE_PREPDE found in conf/modules.config and Nextflow scripts.
modules_config - CIRIQUANT_DE found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC 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 2024-12-16 09:09:03

Versioning

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

Combine beds bugfixes

Max shift plots

Make sure per-sample-tool bed files are non-empty

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 added 23 commits August 2, 2024 22:20

Add annotation back to discovery

baf6d37

Improve annotation output formatting

2ff430e

Remove unnecessary outputs from circrna_discovery

c8fc5c3

Fix bug in tool filtering

b19813a

Prevent pipeline from failing if no circRNAs are found

1f00d9f

Improve annotation output format

35ef315

Remove traces of old merging functionality

d153402

Make sure pipeline fails in an ordered way if no circRNAs are found

eeb1895

Improve error message for no circRNAs found

9bf0609

Linting

ccd0bda

Update first section of introduction

ddbd2f5

Update credits

f8ce1a6

Restructure usage docs

17c692d

Add plans for future implementations to README

1982098

Rename CIRCRNA_DISCOVERY to BSJ_DETECTION

9e9fdd9

Rename params.tool to params.tools

532c956

Remove unused species_id parameter

ac23046

Apply parameter changes to test configs

fde46d0

Change some default values

a808527

Finish updating usage docs

9f6a709

Add output directory structure documentation

b0f797b

Add documentation for references output

5bdd08b

Improve STAR output documentation

bd08029

nictru and others added 30 commits October 10, 2024 12:33

Consider strand in bed aggregation

e87473c

Add consider_strand parameter

5fca06f

Change default of consider_strand in nextflow_schema

4cb2b17

Standardize consider_strand implementation

30daac4

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

Merge pull request #177 from nf-core/combine_beds-bugfixes

7e01b25

Combine beds bugfixes

Add first version of the max-shift plots

3e1af66

Update plot description

7d1e551

Improve max-shift plots

25d4c9a

Merge pull request #178 from nf-core/max-shift-plots

1e16e22

Max shift plots

Make sure per-sample-tool bed files are non-empty

b49b8e1

Merge pull request #180 from nf-core/empty-annotation-intersection

abdc4cb

Make sure per-sample-tool bed files are non-empty

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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

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❌ Test failures:

❗ Test warnings:

✅ Tests passed:

Run details

v1.0.0 #66

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v1.0.0 #66

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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 pipelines lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

✅ Tests passed:

Run details

Python linting (`black`) is failing

github-actions bot commented Feb 2, 2024 •

edited

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