Fix salmon files and add tips to docs #598

lpantano · 2021-04-16T20:05:05Z

Add documentation to guide the analysis from salmon output files - [slack discussion]
[#575] - Remove duplicated salmon output files.
[#585] - Clarify salmon uncertainty for some transcripts.

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!
Make sure your code lints (nf-core lint .).
Ensure the test suite passes (nextflow run . -profile test,docker).
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.

github-actions · 2021-04-16T20:06:26Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 596a8ef

+| ✅ 106 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

files_exist - File not found: environment.yml
files_exist - File not found: Dockerfile
nextflow_config - Config variable not found: process.container
readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

files_exist - File is ignored: bin/markdown_to_html.py
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
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 does not exist: bin/markdown_to_html.py
files_unchanged - File ignored due to lint config: lib/NfcoreSchema.groovy
files_unchanged - File does not exist: .github/workflows/push_dockerhub_dev.yml
files_unchanged - File does not exist: .github/workflows/push_dockerhub_release.yml
files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml
actions_awsfulltest - actions_awsfulltest
conda_env_yaml - No environment.yml file found - skipping conda_env_yaml test
conda_dockerfile - No environment.yml / Dockerfile file found - skipping conda_dockerfile test

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: CHANGELOG.md
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
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.md
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File found: .github/markdownlint.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.png
files_exist - File found: docs/images/nf-core-rnaseq_logo.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: main.nf
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 not found check: Singularity
files_exist - File not found check: parameters.settings.json
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: .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: 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.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 .svg
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: '3.1dev'
files_unchanged - .gitattributes 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.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.md matches the template
files_unchanged - .github/markdownlint.yml matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-rnaseq_logo.png matches the template
files_unchanged - docs/images/nf-core-rnaseq_logo.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - .gitignore 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
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (231 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: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files

Run details

nf-core/tools version 1.13.3
Run at 2021-04-16 20:06:03

j-andrews7 · 2021-04-16T21:24:06Z

This looks good to me, thanks @lpantano!

drpatelh · 2021-04-16T22:26:50Z

Fantastico!!

Lorena Pantano added 2 commits April 16, 2021 16:02

Clean salmon output files and add tips in docs

934e50a

mention changes

596a8ef

drpatelh marked this pull request as ready for review April 16, 2021 22:26

drpatelh approved these changes Apr 16, 2021

View reviewed changes

drpatelh merged commit 4c27ef5 into dev Apr 16, 2021

This was referenced Apr 16, 2021

Remove redundant salmon TPM output #575

Closed

Rdata object "deseq2.dds.RData" and gene count matrix "salmon.merged.gene_counts.tsv" not consistent between 2 runs on same data #585

Closed

drpatelh deleted the patch-salmon-files branch June 18, 2021 08:10

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Fix salmon files and add tips to docs #598

Fix salmon files and add tips to docs #598

lpantano commented Apr 16, 2021 •

edited

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github-actions bot commented Apr 16, 2021 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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j-andrews7 commented Apr 16, 2021

drpatelh commented Apr 16, 2021

Fix salmon files and add tips to docs #598

Fix salmon files and add tips to docs #598

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lpantano commented Apr 16, 2021 • edited Loading

PR checklist

github-actions bot commented Apr 16, 2021 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

j-andrews7 commented Apr 16, 2021

drpatelh commented Apr 16, 2021

lpantano commented Apr 16, 2021 •

edited

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github-actions bot commented Apr 16, 2021 •

edited

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`nf-core lint` overall result: Passed ✅ ⚠️