Updates to adapt pipeline to new template (This also include PR #142 Implementation of IsoformSwitchAnalyzeR)

[lathikaa]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/rnasplice branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8dcff23

+| ✅ 277 tests passed       |+
!| ❗   8 tests had warnings |!

❗ Test warnings:

• files_exist - File not found: conf/igenomes_ignored.config
• nextflow_config - Config manifest.version should end in dev: 1.0.5
• 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: 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-rnasplice_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-rnasplice_logo_light.png
• files_exist - File found: docs/images/nf-core-rnasplice_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-rnasplice_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/WorkflowRnasplice.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.source= fastq
• nextflow_config - Config default value correct: params.gtf_extra_attributes= gene_name
• nextflow_config - Config default value correct: params.gtf_group_features= gene_id
• 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.min_trimmed_reads= 10000
• nextflow_config - Config default value correct: params.skip_bigwig= true
• nextflow_config - Config default value correct: params.aligner= star_salmon
• nextflow_config - Config default value correct: params.pseudo_aligner= salmon
• nextflow_config - Config default value correct: params.rmats= true
• nextflow_config - Config default value correct: params.rmats_splice_diff_cutoff= 0.0001
• nextflow_config - Config default value correct: params.rmats_paired_stats= true
• nextflow_config - Config default value correct: params.rmats_read_len= 40
• nextflow_config - Config default value correct: params.rmats_min_intron_len= 50
• nextflow_config - Config default value correct: params.rmats_max_exon_len= 500
• nextflow_config - Config default value correct: params.dexseq_exon= true
• nextflow_config - Config default value correct: params.alignment_quality= 10
• nextflow_config - Config default value correct: params.aggregation= true
• nextflow_config - Config default value correct: params.save_dexseq_plot= true
• nextflow_config - Config default value correct: params.n_dexseq_plot= 10
• nextflow_config - Config default value correct: params.edger_exon= true
• nextflow_config - Config default value correct: params.save_edger_plot= true
• nextflow_config - Config default value correct: params.n_edger_plot= 10
• nextflow_config - Config default value correct: params.dexseq_dtu= true
• nextflow_config - Config default value correct: params.dtu_txi= dtuScaledTPM
• nextflow_config - Config default value correct: params.min_samps_gene_expr= 4
• nextflow_config - Config default value correct: params.min_samps_feature_expr= 2
• nextflow_config - Config default value correct: params.min_samps_feature_prop= 2
• nextflow_config - Config default value correct: params.min_gene_expr= 10
• nextflow_config - Config default value correct: params.min_feature_expr= 10
• nextflow_config - Config default value correct: params.min_feature_prop= 0.1
• nextflow_config - Config default value correct: params.sashimi_plot= true
• nextflow_config - Config default value correct: params.miso_genes= ENSG00000004961, ENSG00000005302, ENSG00000147403
• nextflow_config - Config default value correct: params.miso_read_len= 75
• nextflow_config - Config default value correct: params.fig_height= 7
• nextflow_config - Config default value correct: params.fig_width= 7
• nextflow_config - Config default value correct: params.suppa= true
• nextflow_config - Config default value correct: params.suppa_per_local_event= true
• nextflow_config - Config default value correct: params.suppa_per_isoform= true
• nextflow_config - Config default value correct: params.generateevents_pool_genes= true
• nextflow_config - Config default value correct: params.generateevents_event_type= SE SS MX RI FL
• nextflow_config - Config default value correct: params.generateevents_boundary= S
• nextflow_config - Config default value correct: params.generateevents_threshold= 10
• nextflow_config - Config default value correct: params.generateevents_exon_length= 100
• nextflow_config - Config default value correct: params.psiperevent_total_filter= 0
• nextflow_config - Config default value correct: params.diffsplice_local_event= true
• nextflow_config - Config default value correct: params.diffsplice_isoform= true
• nextflow_config - Config default value correct: params.diffsplice_method= empirical
• nextflow_config - Config default value correct: params.diffsplice_area= 1000
• nextflow_config - Config default value correct: params.diffsplice_lower_bound= 0
• nextflow_config - Config default value correct: params.diffsplice_gene_correction= true
• nextflow_config - Config default value correct: params.diffsplice_paired= true
• nextflow_config - Config default value correct: params.diffsplice_alpha= 0.05
• nextflow_config - Config default value correct: params.diffsplice_tpm_threshold= 0
• nextflow_config - Config default value correct: params.diffsplice_nan_threshold= 0
• nextflow_config - Config default value correct: params.clusterevents_local_event= true
• nextflow_config - Config default value correct: params.clusterevents_isoform= true
• nextflow_config - Config default value correct: params.clusterevents_dpsithreshold= 0.05
• nextflow_config - Config default value correct: params.clusterevents_eps= 0.05
• nextflow_config - Config default value correct: params.clusterevents_metric= euclidean
• nextflow_config - Config default value correct: params.clusterevents_min_pts= 20
• nextflow_config - Config default value correct: params.clusterevents_method= DBSCAN
• nextflow_config - Config default value correct: params.isoformswitchanalyzer= true
• nextflow_config - Config default value correct: params.isoformswitchanalyzer_alpha= 0.05
• nextflow_config - Config default value correct: params.isoformswitchanalyzer_dIF= 0.1
• 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-rnasplice_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-rnasplice_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-rnasplice_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
• readme - README Zenodo placeholder was replaced with DOI.
• 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: 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.
• base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - SAMPLESHEET_CHECK found in conf/modules.config and Nextflow scripts.
• modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
• modules_config - GUNZIP_ found in conf/modules.config and Nextflow scripts.
• modules_config - UNTAR_ found in conf/modules.config and Nextflow scripts.
• modules_config - UNTAR_ found in conf/modules.config and Nextflow scripts.
• modules_config - GFFREAD found in conf/modules.config and Nextflow scripts.
• modules_config - GFFREAD_TX2GENE found in conf/modules.config and Nextflow scripts.
• modules_config - SALMON_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - CAT_FASTQ found in conf/modules.config and Nextflow scripts.
• modules_config - CUSTOM_GETCHROMSIZES found in conf/modules.config and Nextflow scripts.
• modules_config - PREPROCESS_TRANSCRIPTS_FASTA_GENCODE found in conf/modules.config and Nextflow scripts.
• modules_config - GTF_GENE_FILTER found in conf/modules.config and Nextflow scripts.
• modules_config - BEDTOOLS_GENOMECOV found in conf/modules.config and Nextflow scripts.
• modules_config - STAR_ALIGN found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_SORT found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - SALMON_QUANT_STAR found in conf/modules.config and Nextflow scripts.
• modules_config - SALMON_QUANT_SALMON found in conf/modules.config and Nextflow scripts.
• modules_config - RMATS_PREP found in conf/modules.config and Nextflow scripts.
• modules_config - CREATE_BAMLIST found in conf/modules.config and Nextflow scripts.
• modules_config - DEXSEQ_ANNOTATION found in conf/modules.config and Nextflow scripts.
• modules_config - DEXSEQ_COUNT found in conf/modules.config and Nextflow scripts.
• modules_config - DEXSEQ_EXON found in conf/modules.config and Nextflow scripts.
• modules_config - SUBREAD_FLATTENGTF found in conf/modules.config and Nextflow scripts.
• modules_config - SUBREAD_FEATURECOUNTS found in conf/modules.config and Nextflow scripts.
• modules_config - EDGER_EXON found in conf/modules.config and Nextflow scripts.
• modules_config - GTF_2_GFF3 found in conf/modules.config and Nextflow scripts.
• modules_config - MISO_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - MISO_RUN found in conf/modules.config and Nextflow scripts.
• modules_config - MISO_SETTINGS found in conf/modules.config and Nextflow scripts.
• modules_config - MISO_SASHIMI 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

Run details

• nf-core/tools version 3.0.2
• Run at 2024-11-04 16:28:07