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Merging template updates2131 #88

Merged
merged 9 commits into from
Apr 11, 2024
Merged

Merging template updates2131 #88

merged 9 commits into from
Apr 11, 2024

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PayamEmami
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The template has been updated to the latest version
Several bug fixes and improvements

  • Default change: negative adducts have been changed to H-1:-:0.8 H-3O-1:-:0.2
  • SIRIUS has been updated to 5.8.6
  • MS2QUERY has been updated to 1.2.3
  • New parameter ignore_msms_mapping_charge_pyopenms has been added to control the MS2 mapping if the charges are inconsistent between the consensus elements and spectra

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/metaboigniter 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>).
  • 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 GitHub Actions
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github-actions bot commented Apr 11, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c63653c

+| ✅ 284 tests passed       |+
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • 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!

✅ 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-metaboigniter_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-metaboigniter_logo_light.png
  • files_exist - File found: docs/images/nf-core-metaboigniter_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: .github/workflows/awstest.yml
  • files_exist - File found: .github/workflows/awsfulltest.yml
  • files_exist - File found: modules.json
  • files_exist - File found: pyproject.toml
  • files_exist - File not found check: Singularity
  • files_exist - File not found check: parameters.settings.json
  • files_exist - File not found check: pipeline_template.yml
  • files_exist - File not found check: .nf-core.yaml
  • 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: .github/workflows/push_dockerhub.yml
  • 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: docs/images/nf-core-metaboigniter_logo.png
  • files_exist - File not found check: .markdownlint.yml
  • files_exist - File not found check: .yamllint.yml
  • 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/Workflow.groovy
  • files_exist - File not found check: lib/Utils.groovy
  • files_exist - File not found check: lib/WorkflowMain.groovy
  • files_exist - File not found check: lib/NfcoreTemplate.groovy
  • files_exist - File not found check: lib/WorkflowMetaboigniter.groovy
  • 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: 2.1.0dev
  • 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.skip_centroiding= true
  • nextflow_config - Config default value correct: params.polarity= positive
  • nextflow_config - Config default value correct: params.ms2_collection_model= paired
  • nextflow_config - Config default value correct: params.models_dir_ms2query= models
  • nextflow_config - Config default value correct: params.mgf_splitmgf_pyopenms= 1
  • nextflow_config - Config default value correct: params.mz_tolerance_pyopenms= 20.0
  • nextflow_config - Config default value correct: params.rt_tolerance_pyopenms= 5.0
  • nextflow_config - Config default value correct: params.annotate_ids_with_subelements_pyopenms= true
  • nextflow_config - Config default value correct: params.measure_from_subelements_pyopenms= true
  • nextflow_config - Config default value correct: params.ignore_msms_mapping_charge_pyopenms= false
  • nextflow_config - Config default value correct: params.ms2_feature_selection= quality
  • nextflow_config - Config default value correct: params.ms2_normalized_intensity= true
  • nextflow_config - Config default value correct: params.ms2_iterations= 3
  • nextflow_config - Config default value correct: params.ms2_ppm_map= 10.0
  • nextflow_config - Config default value correct: params.sirius_project_maxmz= -1.0
  • nextflow_config - Config default value correct: params.sirius_project_loglevel= WARNING
  • nextflow_config - Config default value correct: params.sirius_sirius_ppm_max= 10.0
  • nextflow_config - Config default value correct: params.sirius_sirius_ppm_max_ms2= 10.0
  • nextflow_config - Config default value correct: params.sirius_sirius_tree_timeout= 100.0
  • nextflow_config - Config default value correct: params.sirius_sirius_compound_timeout= 100.0
  • nextflow_config - Config default value correct: params.sirius_sirius_profile= default
  • nextflow_config - Config default value correct: params.sirius_sirius_candidates= 10
  • nextflow_config - Config default value correct: params.sirius_sirius_candidates_per_ion= 1
  • nextflow_config - Config default value correct: params.sirius_sirius_elements_considered= SBrClBSe
  • nextflow_config - Config default value correct: params.sirius_sirius_elements_enforced= CHNOP
  • nextflow_config - Config default value correct: params.sirius_sirius_ions_considered= [M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-
  • nextflow_config - Config default value correct: params.sirius_sirius_solver= CLP
  • nextflow_config - Config default value correct: params.split_consensus_parts= 20
  • nextflow_config - Config default value correct: params.algorithm_metabolitefeaturedeconvolution_charge_min_metaboliteadductdecharger_openms= 1
  • nextflow_config - Config default value correct: params.algorithm_metabolitefeaturedeconvolution_charge_max_metaboliteadductdecharger_openms= 1
  • nextflow_config - Config default value correct: params.algorithm_metabolitefeaturedeconvolution_charge_span_max_metaboliteadductdecharger_openms= 1
  • nextflow_config - Config default value correct: params.algorithm_metabolitefeaturedeconvolution_q_try_metaboliteadductdecharger_openms= feature
  • nextflow_config - Config default value correct: params.algorithm_metabolitefeaturedeconvolution_retention_max_diff_metaboliteadductdecharger_openms= 1.0
  • nextflow_config - Config default value correct: params.algorithm_metabolitefeaturedeconvolution_retention_max_diff_local_metaboliteadductdecharger_openms= 1.0
  • nextflow_config - Config default value correct: params.algorithm_metabolitefeaturedeconvolution_mass_max_diff_metaboliteadductdecharger_openms= 5.0
  • nextflow_config - Config default value correct: params.algorithm_metabolitefeaturedeconvolution_unit_metaboliteadductdecharger_openms= ppm
  • nextflow_config - Config default value correct: params.algorithm_metabolitefeaturedeconvolution_max_neutrals_metaboliteadductdecharger_openms= 1
  • nextflow_config - Config default value correct: params.algorithm_metabolitefeaturedeconvolution_use_minority_bound_metaboliteadductdecharger_openms= true
  • nextflow_config - Config default value correct: params.algorithm_metabolitefeaturedeconvolution_max_minority_bound_metaboliteadductdecharger_openms= 1
  • nextflow_config - Config default value correct: params.algorithm_metabolitefeaturedeconvolution_min_rt_overlap_metaboliteadductdecharger_openms= 0.66
  • nextflow_config - Config default value correct: params.algorithm_metabolitefeaturedeconvolution_default_map_label_metaboliteadductdecharger_openms= decharged features
  • nextflow_config - Config default value correct: params.adducts_pos= H:+:0.6 Na:+:0.1 NH4:+:0.1 H-1O-1:+:0.1 H-3O-2:+:0.1
  • nextflow_config - Config default value correct: params.adducts_neg= H-1:-:0.8 H-3O-1:-:0.2
  • nextflow_config - Config default value correct: params.algorithm_max_num_peaks_considered_mapalignerposeclustering_openms= 1000
  • nextflow_config - Config default value correct: params.algorithm_superimposer_mz_pair_max_distance_mapalignerposeclustering_openms= 0.5
  • nextflow_config - Config default value correct: params.algorithm_superimposer_rt_pair_distance_fraction_mapalignerposeclustering_openms= 0.1
  • nextflow_config - Config default value correct: params.algorithm_superimposer_num_used_points_mapalignerposeclustering_openms= 2000
  • nextflow_config - Config default value correct: params.algorithm_superimposer_scaling_bucket_size_mapalignerposeclustering_openms= 0.005
  • nextflow_config - Config default value correct: params.algorithm_pairfinder_ignore_adduct_mapalignerposeclustering_openms= true
  • nextflow_config - Config default value correct: params.algorithm_pairfinder_distance_rt_max_difference_mapalignerposeclustering_openms= 100.0
  • nextflow_config - Config default value correct: params.algorithm_pairfinder_distance_mz_max_difference_mapalignerposeclustering_openms= 0.3
  • nextflow_config - Config default value correct: params.algorithm_pairfinder_distance_mz_unit_mapalignerposeclustering_openms= Da
  • nextflow_config - Config default value correct: params.algorithm_pairfinder_distance_intensity_log_transform_mapalignerposeclustering_openms= disabled
  • nextflow_config - Config default value correct: params.algorithm_mz_unit_featurelinkerunlabeledkd_openms= ppm
  • nextflow_config - Config default value correct: params.algorithm_nr_partitions_featurelinkerunlabeledkd_openms= 100
  • nextflow_config - Config default value correct: params.algorithm_warp_enabled_featurelinkerunlabeledkd_openms= true
  • nextflow_config - Config default value correct: params.algorithm_warp_rt_tol_featurelinkerunlabeledkd_openms= 100.0
  • nextflow_config - Config default value correct: params.algorithm_warp_mz_tol_featurelinkerunlabeledkd_openms= 5.0
  • nextflow_config - Config default value correct: params.algorithm_warp_max_pairwise_log_fc_featurelinkerunlabeledkd_openms= 0.5
  • nextflow_config - Config default value correct: params.algorithm_warp_min_rel_cc_size_featurelinkerunlabeledkd_openms= 0.5
  • nextflow_config - Config default value correct: params.algorithm_warp_max_nr_conflicts_featurelinkerunlabeledkd_openms= 0
  • nextflow_config - Config default value correct: params.algorithm_link_rt_tol_featurelinkerunlabeledkd_openms= 30.0
  • nextflow_config - Config default value correct: params.algorithm_link_mz_tol_featurelinkerunlabeledkd_openms= 10.0
  • nextflow_config - Config default value correct: params.algorithm_link_charge_merging_featurelinkerunlabeledkd_openms= With_charge_zero
  • nextflow_config - Config default value correct: params.algorithm_link_adduct_merging_featurelinkerunlabeledkd_openms= Any
  • nextflow_config - Config default value correct: params.algorithm_distance_rt_exponent_featurelinkerunlabeledkd_openms= 1.0
  • nextflow_config - Config default value correct: params.algorithm_distance_rt_weight_featurelinkerunlabeledkd_openms= 1.0
  • nextflow_config - Config default value correct: params.algorithm_distance_mz_exponent_featurelinkerunlabeledkd_openms= 2.0
  • nextflow_config - Config default value correct: params.algorithm_distance_mz_weight_featurelinkerunlabeledkd_openms= 1.0
  • nextflow_config - Config default value correct: params.algorithm_distance_intensity_exponent_featurelinkerunlabeledkd_openms= 1.0
  • nextflow_config - Config default value correct: params.algorithm_distance_intensity_weight_featurelinkerunlabeledkd_openms= 1.0
  • nextflow_config - Config default value correct: params.algorithm_distance_intensity_log_transform_featurelinkerunlabeledkd_openms= enabled
  • nextflow_config - Config default value correct: params.algorithm_lowess_span_featurelinkerunlabeledkd_openms= 0.666666666666667
  • nextflow_config - Config default value correct: params.algorithm_lowess_num_iterations_featurelinkerunlabeledkd_openms= 3
  • nextflow_config - Config default value correct: params.algorithm_lowess_delta_featurelinkerunlabeledkd_openms= -1.0
  • nextflow_config - Config default value correct: params.algorithm_lowess_interpolation_type_featurelinkerunlabeledkd_openms= cspline
  • nextflow_config - Config default value correct: params.algorithm_lowess_extrapolation_type_featurelinkerunlabeledkd_openms= four-point-linear
  • nextflow_config - Config default value correct: params.model_type_maprttransformer_openms= none
  • nextflow_config - Config default value correct: params.model_linear_x_weight_maprttransformer_openms= x
  • nextflow_config - Config default value correct: params.model_linear_y_weight_maprttransformer_openms= y
  • nextflow_config - Config default value correct: params.model_linear_x_datum_min_maprttransformer_openms= 1e-15
  • nextflow_config - Config default value correct: params.model_linear_x_datum_max_maprttransformer_openms= 1000000000000000.0
  • nextflow_config - Config default value correct: params.model_linear_y_datum_min_maprttransformer_openms= 1e-15
  • nextflow_config - Config default value correct: params.model_linear_y_datum_max_maprttransformer_openms= 1000000000000000.0
  • nextflow_config - Config default value correct: params.model_b_spline_extrapolate_maprttransformer_openms= linear
  • nextflow_config - Config default value correct: params.model_lowess_delta_maprttransformer_openms= -1.0
  • nextflow_config - Config default value correct: params.model_lowess_interpolation_type_maprttransformer_openms= cspline
  • nextflow_config - Config default value correct: params.model_lowess_extrapolation_type_maprttransformer_openms= four-point-linear
  • nextflow_config - Config default value correct: params.model_interpolated_interpolation_type_maprttransformer_openms= cspline
  • nextflow_config - Config default value correct: params.model_interpolated_extrapolation_type_maprttransformer_openms= two-point-linear
  • nextflow_config - Config default value correct: params.model_type_featurefindermetaboident_openms= symmetric
  • nextflow_config - Config default value correct: params.algorithm_report_fwhm_unit_peakpickerhires_openms= relative
  • nextflow_config - Config default value correct: params.algorithm_signaltonoise_noise_for_empty_window_peakpickerhires_openms= 1e+20
  • nextflow_config - Config default value correct: params.algorithm_common_noise_threshold_int_featurefindermetabo_openms= 10.0
  • nextflow_config - Config default value correct: params.algorithm_common_chrom_peak_snr_featurefindermetabo_openms= 3.0
  • nextflow_config - Config default value correct: params.algorithm_common_chrom_fwhm_featurefindermetabo_openms= 5.0
  • nextflow_config - Config default value correct: params.algorithm_mtd_mass_error_ppm_featurefindermetabo_openms= 20.0
  • nextflow_config - Config default value correct: params.algorithm_mtd_reestimate_mt_sd_featurefindermetabo_openms= true
  • nextflow_config - Config default value correct: params.algorithm_mtd_quant_method_featurefindermetabo_openms= area
  • nextflow_config - Config default value correct: params.algorithm_mtd_trace_termination_criterion_featurefindermetabo_openms= outlier
  • nextflow_config - Config default value correct: params.algorithm_mtd_trace_termination_outliers_featurefindermetabo_openms= 5
  • nextflow_config - Config default value correct: params.algorithm_mtd_min_sample_rate_featurefindermetabo_openms= 0.5
  • nextflow_config - Config default value correct: params.algorithm_mtd_min_trace_length_featurefindermetabo_openms= 5.0
  • nextflow_config - Config default value correct: params.algorithm_mtd_max_trace_length_featurefindermetabo_openms= -1.0
  • nextflow_config - Config default value correct: params.algorithm_epd_enabled_featurefindermetabo_openms= true
  • nextflow_config - Config default value correct: params.algorithm_epd_width_filtering_featurefindermetabo_openms= fixed
  • nextflow_config - Config default value correct: params.algorithm_epd_min_fwhm_featurefindermetabo_openms= 1.0
  • nextflow_config - Config default value correct: params.algorithm_epd_max_fwhm_featurefindermetabo_openms= 60.0
  • nextflow_config - Config default value correct: params.algorithm_ffm_local_rt_range_featurefindermetabo_openms= 10.0
  • nextflow_config - Config default value correct: params.algorithm_ffm_local_mz_range_featurefindermetabo_openms= 6.5
  • nextflow_config - Config default value correct: params.algorithm_ffm_charge_lower_bound_featurefindermetabo_openms= 1
  • nextflow_config - Config default value correct: params.algorithm_ffm_charge_upper_bound_featurefindermetabo_openms= 1
  • nextflow_config - Config default value correct: params.algorithm_ffm_enable_rt_filtering_featurefindermetabo_openms= true
  • nextflow_config - Config default value correct: params.algorithm_ffm_isotope_filtering_model_featurefindermetabo_openms= metabolites (5% RMS)
  • nextflow_config - Config default value correct: params.algorithm_ffm_use_smoothed_intensities_featurefindermetabo_openms= true
  • nextflow_config - Config default value correct: params.algorithm_ffm_elements_featurefindermetabo_openms= CHNOPS
  • 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= 16
  • nextflow_config - Config default value correct: params.max_memory= 128.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.validate_params= true
  • nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
  • 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-metaboigniter_logo_light.png matches the template
  • files_unchanged - docs/images/nf-core-metaboigniter_logo_light.png matches the template
  • files_unchanged - docs/images/nf-core-metaboigniter_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
  • files_unchanged - pyproject.toml 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
  • readme - README Zenodo placeholder was replaced with DOI.
  • pipeline_name_conventions - Name adheres to nf-core convention
  • template_strings - Did not find any Jinja template strings (171 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: fix-linting.yml
  • actions_schema_validation - Workflow validation passed: awsfulltest.yml
  • actions_schema_validation - Workflow validation passed: awstest.yml
  • actions_schema_validation - Workflow validation passed: release-announcements.yml
  • actions_schema_validation - Workflow validation passed: linting_comment.yml
  • actions_schema_validation - Workflow validation passed: ci.yml
  • actions_schema_validation - Workflow validation passed: download_pipeline.yml
  • actions_schema_validation - Workflow validation passed: clean-up.yml
  • actions_schema_validation - Workflow validation passed: linting.yml
  • actions_schema_validation - Workflow validation passed: branch.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' 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'

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-11 11:11:27

@PayamEmami
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This also resolves
#86
#83
#80
#78

@PayamEmami PayamEmami merged commit bb3a1f7 into nf-core:dev Apr 11, 2024
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@axelwalter axelwalter axelwalter approved these changes

@AinaVaivade AinaVaivade Awaiting requested review from AinaVaivade

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@PayamEmami @axelwalter @nf-core-bot