v1.0.0

[BarryDigby]

DSL2 version of nf-core/circrna.

A few minor comments on the linting warnings:

1. I need some assistance configuring the full AWS test dataset. The data can be accessed via SRA, this should be straightforward using fetchngs.

2. 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]

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]

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

[github-actions]

nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 1a64623

+| ✅ 268 tests passed       |+
!| ❗  11 tests had warnings |!
-| ❌   3 tests failed       |-

Details

❌ 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 nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
• pipeline_todos - TODO string in ro-crate-metadata.json: "description": "

  \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-circrna_logo_dark.png">\n <img alt="nf-core/circrna" src="docs/images/nf-core-circrna_logo_light.png">\n \n

  \n\n\n\n\n\n\n\n\n\n\n\n## Introduction\n\nnf-core/circrna is a bioinformatics pipeline that ...\n\n TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n\n\n Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. \n Fill in short bullet-pointed list of the default steps in the pipeline 1. Read QC (FastQC)2. Present QC for raw reads (MultiQC)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.Make sure to test your setup with -profile test before running the workflow on actual data.\n\n Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\nsamplesheet.csv:\n\ncsv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n\n\nNow, you can run the pipeline using:\n\n update the following command to include all required parameters for a minimal example \n\nbash\nnextflow run nf-core/circrna \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.\n\nFor more details and further functionality, please refer to the usage documentation and the parameter documentation.\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\noutput documentation.\n\n## Credits\n\nnf-core/circrna was originally written by Barry Digby, Nico Trummer.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n If applicable, make list of people who have also contributed \n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the contributing guidelines.\n\nFor further information or help, don't hesitate to get in touch on the Slack #circrna channel (you can join with this invite).\n\n## Citations\n\n Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. \n If you use nf-core/circrna for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX Add bibliography of tools and data used in your pipeline \n\nAn extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.\n\nYou can cite the nf-core publication as follows:\n\n> The nf-core framework for community-curated bioinformatics pipelines.\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.\n",
• 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 base.config: Check the defaults for all processes
• 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
• 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

✅ 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 found: ro-crate-metadata.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: branch.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: template_version_comment.yml
• actions_schema_validation - Workflow validation passed: 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: fix-linting.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 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 - UCSC_GTFTOGENEPRED 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 - CIRCEXPLORER2_REFERENCE 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: 3.1.1
• version_consistency - Version tags are numeric and consistent between container, release tag and config.

Run details

• nf-core/tools version 3.1.1
• Run at 2025-01-30 13:05:35