Remove synapse workflow from pipeline

[drpatelh]

Support for Synapse ids has been dropped in this release. We haven't had any feedback from users whether it is being used or not. Users can run earlier versions of the pipeline if required.

[github-actions]

nf-core lint overall result: Failed ❌

Posted for pipeline commit 3e825cc

+| ✅ 147 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

• files_unchanged - .gitignore does not match the template

❗ Test warnings:

• files_exist - File not found: assets/multiqc_config.yml
• files_exist - File not found: conf/igenomes.config
• files_exist - File not found: .github/workflows/awstest.yml
• files_exist - File not found: .github/workflows/awsfulltest.yml
• files_exist - File not found: lib/WorkflowFetchngs.groovy
• nextflow_config - Config manifest.version should end in dev: 1.12.0
• 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 ignored:

• files_exist - File is ignored: conf/modules.config
• files_exist - File is ignored: lib/NfcoreTemplate.groovy
• files_exist - File is ignored: lib/Utils.groovy
• files_exist - File is ignored: lib/WorkflowMain.groovy
• files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
• files_unchanged - File does not exist: lib/NfcoreTemplate.groovy
• actions_ci - actions_ci
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchngs/fetchngs/.github/workflows/awstest.yml
• multiqc_config - 'assets/multiqc_config.yml' not found

✅ 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-fetchngs_logo_light.png
• files_exist - File found: conf/test.config
• files_exist - File found: conf/test_full.config
• files_exist - File found: docs/images/nf-core-fetchngs_logo_light.png
• files_exist - File found: docs/images/nf-core-fetchngs_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: conf/base.config
• 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-fetchngs_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/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 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.sample_mapping_fields= experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description
• nextflow_config - Config default value correct: params.nf_core_rnaseq_strandedness= auto
• 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
• 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/nf-core-fetchngs_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-fetchngs_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-fetchngs_logo_dark.png matches the template
• files_unchanged - docs/README.md matches the template
• files_unchanged - .prettierignore matches the template
• files_unchanged - pyproject.toml matches the template
• 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 (148 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: release-announcements.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: cloud_tests_small.yml
• actions_schema_validation - Workflow validation passed: cloud_tests_full.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: clean-up.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
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

• nf-core/tools version 2.12.1
• Run at 2024-02-01 11:16:53

[maxulysse]

Loving this idea, synapse was also a mess to test out CI wise