rnaseq
rnaseq copied to clipboard
convert `console` snippets to `bash` snippets where applicable
console snippets are in general only nice to display terminal outputs, not anything related to scripts or commands.
PR checklist
- [x] This comment contains a description of changes (with reason).
nf-core lint overall result: Passed :white_check_mark: :warning:
Posted for pipeline commit c546bf1
+| ✅ 145 tests passed |+
#| ❔ 3 tests were ignored |#
!| ❗ 1 tests had warnings |!
:heavy_exclamation_mark: Test warnings:
- readme - README did not have a Nextflow minimum version badge.
:grey_question: Tests ignored:
- files_unchanged - File ignored due to lint config:
assets/email_template.html - files_unchanged - File ignored due to lint config:
assets/email_template.txt - files_unchanged - File ignored due to lint config:
lib/NfcoreTemplate.groovy
:white_check_mark: 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:
.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:
CODE_OF_CONDUCT.md - files_exist - File found:
LICENSEorLICENSE.mdorLICENCEorLICENCE.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-rnaseq_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-rnaseq_logo_light.png - files_exist - File found:
docs/images/nf-core-rnaseq_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:
lib/nfcore_external_java_deps.jar - files_exist - File found:
lib/NfcoreSchema.groovy - files_exist - File found:
lib/NfcoreTemplate.groovy - files_exist - File found:
lib/Utils.groovy - files_exist - File found:
lib/WorkflowMain.groovy - 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:
lib/WorkflowRnaseq.groovy - files_exist - File found:
modules.json - files_exist - File not found check:
Singularity - files_exist - File not found check:
parameters.settings.json - 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-rnaseq_logo.png - files_exist - File not found check:
.markdownlint.yml - files_exist - File not found check:
.yamllint.yml - 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.show_hidden_params - nextflow_config - Config variable found:
params.schema_ignore_params - 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.version - 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
timeline.enabledhad correct value:true - nextflow_config - Config
report.enabledhad correct value:true - nextflow_config - Config
trace.enabledhad correct value:true - nextflow_config - Config
dag.enabledhad correct value:true - nextflow_config - Config
manifest.namebegan withnf-core/ - nextflow_config - Config variable
manifest.homePagebegan with https://github.com/nf-core/ - nextflow_config - Config
dag.fileended with.html - nextflow_config - Config variable
manifest.nextflowVersionstarted with >= or !>= - nextflow_config - Config
manifest.versionends indev:'3.9dev' - nextflow_config - Config
params.custom_config_versionis set tomaster - nextflow_config - Config
params.custom_config_baseis set tohttps://raw.githubusercontent.com/nf-core/configs/master - nextflow_config - Lines for loading custom profiles found
- files_unchanged -
.gitattributesmatches the template - files_unchanged -
.prettierrc.ymlmatches the template - files_unchanged -
CODE_OF_CONDUCT.mdmatches the template - files_unchanged -
LICENSEmatches the template - files_unchanged -
.github/.dockstore.ymlmatches the template - files_unchanged -
.github/CONTRIBUTING.mdmatches the template - files_unchanged -
.github/ISSUE_TEMPLATE/bug_report.ymlmatches the template - files_unchanged -
.github/ISSUE_TEMPLATE/config.ymlmatches the template - files_unchanged -
.github/ISSUE_TEMPLATE/feature_request.ymlmatches the template - files_unchanged -
.github/PULL_REQUEST_TEMPLATE.mdmatches the template - files_unchanged -
.github/workflows/branch.ymlmatches the template - files_unchanged -
.github/workflows/linting_comment.ymlmatches the template - files_unchanged -
.github/workflows/linting.ymlmatches the template - files_unchanged -
assets/sendmail_template.txtmatches the template - files_unchanged -
assets/nf-core-rnaseq_logo_light.pngmatches the template - files_unchanged -
docs/images/nf-core-rnaseq_logo_light.pngmatches the template - files_unchanged -
docs/images/nf-core-rnaseq_logo_dark.pngmatches the template - files_unchanged -
docs/README.mdmatches the template - files_unchanged -
lib/nfcore_external_java_deps.jarmatches the template - files_unchanged -
lib/NfcoreSchema.groovymatches the template - files_unchanged -
.gitignorematches 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.ymlis triggered correctly - actions_awsfulltest -
.github/workflows/awsfulltest.ymldoes not use-profile test - readme - README Nextflow minimum version in Quick Start section matched config. README:
21.10.3, Config:21.10.3 - pipeline_todos - No TODO strings found
- pipeline_name_conventions - Name adheres to nf-core convention
- template_strings - Did not find any Jinja template strings (215 files)
- schema_lint - Schema lint passed
- schema_lint - Schema title + description lint passed
- schema_params - Schema matched params returned from nextflow config
- actions_schema_validation - Workflow validation passed: linting.yml
- actions_schema_validation - Workflow validation passed: ci.yml
- actions_schema_validation - Workflow validation passed: awsfulltest.yml
- actions_schema_validation - Workflow validation passed: awstest.yml
- actions_schema_validation - Workflow validation passed: linting_comment.yml
- actions_schema_validation - Workflow validation passed: branch.yml
- actions_schema_validation - Workflow validation passed: fix-linting.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' 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'.
Run details
- nf-core/tools version 2.4.1
- Run at
2022-08-03 14:33:36
I don't know why but I can't see any Files changed

Although I can see in the commits that you applied some changes 🤔
hmm, maybe my git revert+push didn't work then? It worked locally... Weird. Can maybe somebody else revert my accidental push and then we see if some changes appear for this PR.
@mashehu want to merge this but there is nothing to merge! 😅