Dev -> Master for 1.6 release #92

drpatelh · 2022-05-16T20:19:35Z

No description provided.

Bump version to 1.6dev

Typo fix for ENA-API URL

Remove igenomes.config remnants from last template sync

Update CHANGELOG after merging template updates

Replace vanilla Linux Biocontainer with Ubuntu

refactor: use nf-core modules for sratools subworkflow

Add troubleshooting section and FTP alternative docs

github-actions · 2022-05-16T20:20:42Z

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

Posted for pipeline commit 922e81c

+| ✅ 143 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: lib/WorkflowFetchngs.groovy
nextflow_config - Config manifest.version should end in dev: '1.6'
readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ 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: 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/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-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: 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: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
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-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: .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 .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
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 - 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 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 (81 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: linting_comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: ci.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'.

Run details

nf-core/tools version 2.4.1
Run at 2022-05-17 10:55:02

drpatelh · 2022-05-16T20:48:26Z

Tests should be fixed when #91 is merged

Follow up fixes to issue #57

Midnighter

Small question, otherwise looks good.

Midnighter · 2022-05-17T08:58:43Z

nextflow.config

+// Load nf-core/fetchngs custom profiles from different institutions.
+// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
+// try {
+//   includeConfig "${params.custom_config_base}/pipeline/fetchngs.config"
+// } catch (Exception e) {
+//   System.err.println("WARNING: Could not load nf-core/config/fetchngs profiles: ${params.custom_config_base}/pipeline/fetchngs.config")
+// }


You adding this again?

Actually, I was going to ask why this was commented, don't remember now

That snippet is commented and included there for convenience just in case someone needs to add a pipeline-specific configuration to nf-core/configs e.g. here. This came in through the template sync yesterday and won't do any harm to have here.

refactor: adjust FASTQ pattern

JoseEspinosa

Awesome job @Midnighter and @drpatelh 🚀

JoseEspinosa · 2022-05-17T09:54:14Z

nextflow.config

+// Load nf-core/fetchngs custom profiles from different institutions.
+// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
+// try {
+//   includeConfig "${params.custom_config_base}/pipeline/fetchngs.config"
+// } catch (Exception e) {
+//   System.err.println("WARNING: Could not load nf-core/config/fetchngs profiles: ${params.custom_config_base}/pipeline/fetchngs.config")
+// }


Actually, I was going to ask why this was commented, don't remember now

Midnighter · 2022-05-17T10:00:01Z

Would like to bring in #93 before a release.

fix: use parameter for publishing mode

drpatelh · 2022-05-17T11:34:29Z

Over to you to merge and create the release @Midnighter 😁

drpatelh and others added 30 commits December 1, 2021 09:32

Bump version to 1.6dev

a6a670e

Merge pull request #63 from drpatelh/refactor

3a66eeb

Bump version to 1.6dev

Fix typo in URL for usage to ENA API

3a402f2

Template update for nf-core/tools version 2.2

7ca1c7a

Fix merge conflicts

dd64876

Merge branch 'nf-core-template-merge-2.2' into dev

f69da47

Replace dodgy logo

4a2e3c4

Merge pull request #65 from jfy133/typo-fix

8c9448a

Typo fix for ENA-API URL

Remove igenomes.config remnants from last template sync

1cf780f

Merge pull request #78 from drpatelh/test

055e7ff

Remove igenomes.config remnants from last template sync

Template update for nf-core/tools version 2.3

d6d7d70

Add troubleshooting section and FTP alternative docs

c1b2abc

fix linting

dca46e6

Template update for nf-core/tools version 2.3.1

17261e3

Template update for nf-core/tools version 2.3.2

2e62a04

Fix merge conflicts

d779c15

Fix prettier

ce7bb86

Update CHANGELOG after merging template updates

82213da

Add --outdir to CI tests

56f37b2

Merge pull request #83 from drpatelh/test

65ea0d7

Update CHANGELOG after merging template updates

Replace vanilla Linux Biocontainer with Ubuntu

456584a

Actually push updated modules

4bf86f2

Use sra-tools container with curl

b635257

Merge pull request #84 from drpatelh/updates

3a795cb

Replace vanilla Linux Biocontainer with Ubuntu

refactor: remove local modules/subworkflows

c735188

chore: install nf-core modules for sratools

3de66f2

refactor: implement new subworkflow

ad15361

chore: add entry to changelog

3630eb6

Merge pull request #89 from nf-core/refactor-sra

094f5f7

refactor: use nf-core modules for sratools subworkflow

Template update for nf-core/tools version 2.4

7676eac

drpatelh and others added 4 commits May 16, 2022 20:57

Fix merge conflicts

ebbf123

Merge branch 'dev' into dev

331df81

Merge pull request #80 from maxibor/dev

ed0f96d

Add troubleshooting section and FTP alternative docs

Follow up fixes to #57

2f260ba

Fix nf-core linting

7086977

drpatelh requested review from Midnighter and JoseEspinosa May 16, 2022 20:47

Merge pull request #91 from drpatelh/updates

1751937

Follow up fixes to issue #57

Midnighter approved these changes May 17, 2022

View reviewed changes

Midnighter added 2 commits May 17, 2022 11:28

fix: use parameter for publishing mode

d023066

refactor: adjust FASTQ pattern

chore: describe change

7f6e492

JoseEspinosa approved these changes May 17, 2022

View reviewed changes

drpatelh added 2 commits May 17, 2022 11:54

Update CHANGELOG.md

e697f22

Merge pull request #93 from nf-core/fix-publishing

922e81c

fix: use parameter for publishing mode

Midnighter merged commit 7b7ab2f into master May 17, 2022

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Dev -> Master for 1.6 release #92

Dev -> Master for 1.6 release #92

drpatelh commented May 16, 2022

github-actions bot commented May 16, 2022 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

drpatelh commented May 16, 2022

Midnighter left a comment

Midnighter May 17, 2022

JoseEspinosa May 17, 2022

drpatelh May 17, 2022

JoseEspinosa left a comment

JoseEspinosa May 17, 2022

Midnighter commented May 17, 2022

drpatelh commented May 17, 2022

Dev -> Master for 1.6 release #92

Dev -> Master for 1.6 release #92

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drpatelh commented May 16, 2022

github-actions bot commented May 16, 2022 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

drpatelh commented May 16, 2022

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Midnighter commented May 17, 2022

drpatelh commented May 17, 2022

github-actions bot commented May 16, 2022 •

edited

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