update intro and usage documentation #396

rannick · 2023-09-11T10:19:01Z

PR checklist

github-actions · 2023-09-11T10:20:40Z

`nf-core lint` overall result: Passed ✅

Posted for pipeline commit 3395388

+| ✅ 158 tests passed       |+

✅ Tests passed:

files_exist - File found: .gitattributes
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files_exist - File found: CHANGELOG.md
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files_exist - File found: CODE_OF_CONDUCT.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
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files_exist - File found: README.md
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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
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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
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nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
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nextflow_config - Config variable found: report.file
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nextflow_config - Config variable (correctly) not found: params.nf_required_version
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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
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nextflow_config - Lines for loading custom profiles found
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files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreTemplate.groovy matches the template
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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_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (193 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: ci.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awsfulltest.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' 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 2.9
Run at 2023-09-13 13:00:07

peterpru

Nice work, it was very difficult to find problems 💯

README.md

docs/output.md

peterpru · 2023-09-13T06:56:11Z

README.md

-| [StringTie](https://github.com/gpertea/stringtie)         | `2.2.1`  |
-
-> Single-end reads are to be use as last-resort. Paired-end reads are recommended. FusionCatcher cannot be used with single-end reads shorter than 130 bp.
+**nf-core/rnafusion** is a bioinformatics best-practice analysis pipeline for RNA sequencing consisting of several tools designed for detecting and visualizing fusion genes.



Maybe it would be nice for potential users to have an overview of what the expected output is in 1-2 sentences? E.g. the output is a report in XX format with fusions from up to five different fusion callers.

peterpru

👍 👍

docs/output.md

Co-authored-by: Peter Pruisscher <[email protected]>

…fusion into update_documentation

update intro and usage documentation

0b02de3

rannick added 3 commits September 11, 2023 16:34

update citations

23945d3

correct copy-paste error

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first steps in output update

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peterpru approved these changes Sep 12, 2023

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rannick added 3 commits September 13, 2023 10:41

update meta descriptions

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refine output

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prettify

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rannick and others added 11 commits September 13, 2023 14:22

Update docs/output.md

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Co-authored-by: Peter Pruisscher <[email protected]>

Update docs/output.md

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Co-authored-by: Peter Pruisscher <[email protected]>

Update docs/output.md

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Co-authored-by: Peter Pruisscher <[email protected]>

Update README.md

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Co-authored-by: Peter Pruisscher <[email protected]>

Update README.md

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Co-authored-by: Peter Pruisscher <[email protected]>

Update README.md

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Co-authored-by: Peter Pruisscher <[email protected]>

Update README.md

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Co-authored-by: Peter Pruisscher <[email protected]>

Update README.md

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Co-authored-by: Peter Pruisscher <[email protected]>

add output info in README

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Merge branch 'update_documentation' of https://github.com/nf-core/rna…

9684893

…fusion into update_documentation

small typos

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rannick merged commit 2bfdb59 into dev Sep 13, 2023

rannick deleted the update_documentation branch September 13, 2023 13:15

rannick mentioned this pull request Sep 13, 2023

Improve documentation #368

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update intro and usage documentation #396

update intro and usage documentation #396

rannick commented Sep 11, 2023

github-actions bot commented Sep 11, 2023 •

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✅ Tests passed:

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peterpru Sep 13, 2023 •

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update intro and usage documentation #396

update intro and usage documentation #396

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rannick commented Sep 11, 2023

PR checklist

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nf-core lint overall result: Passed ✅

✅ Tests passed:

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github-actions bot commented Sep 11, 2023 •

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`nf-core lint` overall result: Passed ✅

peterpru Sep 13, 2023 •

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