Add Prodigal #240

AntoniaSchuster · 2021-10-28T12:43:50Z

Added Prodigal for protein-coding gene prediction. Closes #239. Not yet implemented: --skip_prodigal

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).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

CHANGELOG.md

Co-authored-by: Daniel Straub <[email protected]>

docs/output.md

github-actions · 2021-10-28T12:59:21Z

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

Posted for pipeline commit 9b7ad0c

+| ✅ 136 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

readme - README did not have a Nextflow minimum version mentioned in Quick Start section.

❔ Tests ignored:

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: .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
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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
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files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
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files_exist - File found: assets/nf-core-mag_logo.png
files_exist - File found: bin/scrape_software_versions.py
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
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files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
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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
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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
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 manifest.version ends in dev: '2.2.0dev'
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 - .markdownlint.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.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/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-mag_logo.png matches the template
files_unchanged - bin/scrape_software_versions.py matches the template
files_unchanged - docs/images/nf-core-mag_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
files_unchanged - assets/multiqc_config.yaml 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 (124 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: linting_comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: ci.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 2021-10-28 14:43:47

docs/output.md

Co-authored-by: Daniel Straub <[email protected]>

conf/modules.config

… assemblers are not overwritten.

CITATIONS.md

d4straub

Looks good to me!

AntoniaSchuster added 2 commits October 28, 2021 13:32

Added nf-core/modules/prodigal

cb64b22

citations, docs and small changes

8b1b288

AntoniaSchuster requested a review from d4straub October 28, 2021 12:43

AntoniaSchuster linked an issue Oct 28, 2021 that may be closed by this pull request

Add Prodigal #239

Closed

AntoniaSchuster added 2 commits October 28, 2021 14:53

Update README and CHANGELOG

adab749

Remove trailing whitespaces

2daeae0