fix testdata file #120

lpantano · 2021-11-23T19:27:27Z

Last bit of the migration, point to the right test data for the current version and update mirtop version container.

PR checklist

This comment contains a description of changes (with reason).
Make sure your code lints (nf-core lint .).
Ensure the test suite passes (nextflow run . -profile test,docker).
CHANGELOG.md is updated.

github-actions · 2021-11-23T19:29:33Z

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

Posted for pipeline commit 59ffb03

+| ✅ 127 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '2.0.0'
readme - README did not have a Nextflow minimum version mentioned in Quick Start section.

❔ Tests ignored:

files_exist - File is ignored: bin/scrape_software_versions.py
files_exist - File is ignored: modules/local/get_software_versions.nf
files_unchanged - File ignored due to lint config: .markdownlint.yml
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
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/scrape_software_versions.py
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .markdownlint.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: 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/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-smrnaseq_logo.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-smrnaseq_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: 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.yaml
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/WorkflowSmrnaseq.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: 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: 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.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 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
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/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/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/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-smrnaseq_logo.png matches the template
files_unchanged - docs/images/nf-core-smrnaseq_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 - lib/NfcoreSchema.groovy 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
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: 21.04.0, Config: 21.04.0
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (118 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: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json

Run details

nf-core/tools version 2.1
Run at 2021-11-23 19:28:59

JoseEspinosa

Just made a small comment regarding the versioning of the sample sheet, otherwise looks good to me 🍬

JoseEspinosa · 2021-11-23T21:05:39Z

CHANGELOG.md

@@ -1,7 +1,9 @@
 # nf-core/smrnaseq: Changelog

-## v1.3.0dev - [2021-09-15]
+## v2.0.0dev - [2021-09-15]


Yes I think a 2.0.0 is justified here!

JoseEspinosa · 2021-11-23T21:08:32Z

conf/test.config

-    mature = 'https://github.com/nf-core/test-datasets/raw/smrnaseq-better-input/reference/mature.fa'
-    hairpin = 'https://github.com/nf-core/test-datasets/raw/smrnaseq-better-input/reference/hairpin.fa'
-    mirna_gtf = 'https://github.com/nf-core/test-datasets/raw/smrnaseq-better-input/reference/hsa.gff3'
+    input = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/testdata/samplesheet.csv'


Maybe we could implement a similar versioning such as in the rnaseq pipeline e.g. https://github.com/nf-core/test-datasets/tree/rnaseq/samplesheet/v3.4

Great idea, especially if some potential future changes are coming in that might have to adjust the format at some point again 👍🏻

ok, should I merge and then coordinate this? or do you want to do it now?

apeltzer · 2021-11-25T09:38:11Z

CHANGELOG.md

@@ -1,7 +1,9 @@
 # nf-core/smrnaseq: Changelog

-## v1.3.0dev - [2021-09-15]
+## v2.0.0dev - [2021-09-15]


Yes I think a 2.0.0 is justified here!

apeltzer · 2021-11-25T09:38:38Z

conf/test.config

-    mature = 'https://github.com/nf-core/test-datasets/raw/smrnaseq-better-input/reference/mature.fa'
-    hairpin = 'https://github.com/nf-core/test-datasets/raw/smrnaseq-better-input/reference/hairpin.fa'
-    mirna_gtf = 'https://github.com/nf-core/test-datasets/raw/smrnaseq-better-input/reference/hsa.gff3'
+    input = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/testdata/samplesheet.csv'


Great idea, especially if some potential future changes are coming in that might have to adjust the format at some point again 👍🏻

JoseEspinosa · 2021-11-30T09:52:15Z

I merge this PR. A new PR will address the requested changes regarding test-datasets versioning 🚀

lpantano added 4 commits November 11, 2021 21:41

add new container for edger

3de3726

Merge branch 'dev' of github.com:nf-core/smrnaseq into dev

0f4da15

fix path to test data

5a65851

update changelog and bump to 2.0.0dev

59ffb03

JoseEspinosa approved these changes Nov 23, 2021

View reviewed changes

apeltzer approved these changes Nov 25, 2021

View reviewed changes

JoseEspinosa merged commit e979ed2 into dev Nov 30, 2021

JoseEspinosa mentioned this pull request Dec 1, 2021

Samplesheet versioning #121

Merged

11 tasks

apeltzer deleted the lpantano-patch-fix-testdata-file branch December 17, 2021 10:50

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fix testdata file #120

fix testdata file #120

lpantano commented Nov 23, 2021

github-actions bot commented Nov 23, 2021 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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JoseEspinosa commented Nov 30, 2021

fix testdata file #120

fix testdata file #120

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lpantano commented Nov 23, 2021

PR checklist

github-actions bot commented Nov 23, 2021 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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JoseEspinosa commented Nov 30, 2021

github-actions bot commented Nov 23, 2021 •

edited

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