Release 2.1.1 by d4straub · Pull Request #261 · nf-core/mag

d4straub · 2021-11-23T12:13:17Z

Current version 2.1.0 doesnt work with the newest nextflow version 21.10.x, so that minor release is needed.
Changes are added Prokka (prokaryotic gene finding & annotation) per MAG, prodigal (prokaryotic gene finding) on metagenome and several bug fixes.

PR checklist

Bump version 2.2.0dev and adjusted release date

Fix workflow diagram CC-BY attribution

fix large assemblies

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

… assemblers are not overwritten.

Add Prodigal

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

Add --skip_prodigal

Co-authored-by: AntoniaSchuster <56543138+AntoniaSchuster@users.noreply.github.com>

…tk-conda

fix gtdbtk conda channel

Add fastp to multiqc

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

Fix --skip_busco

Prepare for release 2.1.1

github-actions · 2021-11-23T12:15:40Z

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

Posted for pipeline commit fda9e23

+| ✅ 135 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '2.1.1'
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
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-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
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-mag_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: modules/local/get_software_versions.nf
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/WorkflowMag.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 - .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 (127 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 2021-11-25 12:03:02

ggabernet

Looks good to me!

jfy133

LGTM 👍

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

d4straub · 2021-11-25T09:33:56Z

Thanks for the reviews! I am running the large test run on our cluster right now, will wait until thats finished before I merge.

jfy133 · 2021-11-25T10:16:44Z

@d4straub beforeyou go, in a separte test I noticed the following typo:

mag/lib/WorkflowMag.groovy

Lines 83 to 119 in 0b51bd1

    
               if (params.skip_busco){ 
        
                   if (params.busco_reference) { 
        
                       log.error "Both --skip_busco and --busco_reference are specififed! Invalid combination, please specify either --skip_busco or --busco_reference." 
        
                       System.exit(1) 
        
                   } 
        
                   if (params.busco_download_path) { 
        
                       log.error "Both --skip_busco and --busco_download_path are specififed! Invalid combination, please specify either --skip_busco or --busco_download_path." 
        
                       System.exit(1) 
        
                   } 
        
                   if (params.busco_auto_lineage_prok) { 
        
                       log.error "Both --skip_busco and --busco_auto_lineage_prok are specififed! Invalid combination, please specify either --skip_busco or --busco_auto_lineage_prok." 
        
                       System.exit(1) 
        
                   } 
        
               } 
        
               if (params.busco_reference && params.busco_download_path) { 
        
                   log.error "Both --busco_reference and --busco_download_path are specififed! Invalid combination, please specify either --busco_reference or --busco_download_path." 
        
                   System.exit(1) 
        
               } 
        
               if (params.busco_auto_lineage_prok && params.busco_reference) { 
        
                   log.error "Both --busco_auto_lineage_prok and --busco_reference are specififed! Invalid combination, please specify either --busco_auto_lineage_prok or --busco_reference." 
        
                   System.exit(1) 
        
               } 
        
               if (params.skip_busco && params.gtdb) { 
        
                   log.warn "--skip_busco and --gtdb are specified! GTDB-tk will be omitted because GTDB-tk bin classification requires bin filtering based on BUSCO QC results to avoid GTDB-tk errors." 
        
               } 
        
               // Check if CAT parameters are valid 
        
               if (params.cat_db && params.cat_db_generate) { 
        
                   log.error "Invalid combination of parameters --cat_db and --cat_db_generate is specififed! Please specify either --cat_db or --cat_db_generate." 
        
                   System.exit(1) 
        
               } 
        
               if (params.save_cat_db && !params.cat_db_generate) { 
        
                   log.error "Invalid parameter combination: parameter --save_cat_db specified, but not --cat_db_generate! Note also that the parameter --save_cat_db does not work in combination with --cat_db." 
        
                   System.exit(1) 
        
               } 
        
           }

specififed -> specified

(this occurs in multiple places in the file, so check everywhere)

d4straub · 2021-11-25T10:56:16Z

Good catch! Seems like a copy paste error, I replaced all occurrences of specififed with specified in #262

jfy133 · 2021-11-25T11:36:59Z

Approved

fix typo

skrakau and others added 30 commits July 29, 2021 15:45

Bump version 2.2.0dev and adjusted release date

b1e5242

Merge pull request #228 from skrakau/bump_2.2.0dev

d4335b1

Bump version 2.2.0dev and adjusted release date

Add correct CC-BY attribution to workflow diagram

3a39e40

fix large assemblies

4fdc450

fix typo

bf0439f

Merge pull request #231 from jfy133/master

6970953

Fix workflow diagram CC-BY attribution

fix centrifuge error

b49357d

Merge pull request #236 from d4straub/dev

d63ce61

fix large assemblies

Added nf-core/modules/prodigal

cb64b22

citations, docs and small changes

8b1b288

Update README and CHANGELOG

adab749

Remove trailing whitespaces

2daeae0

Update CHANGELOG.md

3799d02

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

Update docs/output.md

f619652

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

Updated output, changed prodigal options so predictions for different…

6825bd0

… assemblers are not overwritten.

Merge branch 'dev' of https://github.com/AntoniaSchuster/mag into dev

5d0103a

update prodigal citation

9b7ad0c

Merge pull request #240 from AntoniaSchuster/dev

bf83c44

Add Prodigal

Implement skip_prodigal

1b70241

Update schema

3d43755

Update CHANGELOG.md

e6ab3de

Remove trailing whitespaces

8694f53

Update CHANGELOG.md

4df589b

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

Update nextflow.config

deb8358

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

Merge pull request #241 from AntoniaSchuster/skip_prodigal

554caee

Add --skip_prodigal

add preprint info

61411b6

nf-core modules install prokka

2646966

fix PR no

73827c3

Update CHANGELOG.md

17a0770

Co-authored-by: AntoniaSchuster <56543138+AntoniaSchuster@users.noreply.github.com>

Add prokka

d59c144

d4straub and others added 19 commits November 22, 2021 12:16

update changelog

5c511e1

fix channel

82a1c86

update changelog

b131da1

Merge branch 'dev' of https://github.com/nf-core/mag into fix-skip_busco

7f6bc44

fix update changelog

2db3c2d

Merge branch 'dev' of https://github.com/nf-core/mag into update-gtdb…

1cf290b

…tk-conda

Merge pull request #255 from d4straub/update-gtdbtk-conda

1e98dd2

fix gtdbtk conda channel

add fastp results to MultiQC

da0a283

speed up test_busco_auto by skipping some steps

b9175dd

fix typo

1bc7d0e

Merge pull request #258 from d4straub/add-fastp-to-multiqc

abe85c9

Add fastp to multiqc

merge upstream

a7f7e9d

change gtdb default to mirror

a9399df

Update lib/WorkflowMag.groovy

b45414b

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

Merge pull request #256 from d4straub/fix-skip_busco

2caec7c

Fix --skip_busco

update SPAdes and MEGAHIT

f405bed

bump version

42ffda6

unify indent

70029fa

Merge pull request #260 from d4straub/dev

5a74dba

Prepare for release 2.1.1

ggabernet approved these changes Nov 25, 2021

View reviewed changes

jfy133 approved these changes Nov 25, 2021

View reviewed changes

Comment thread CHANGELOG.md Outdated

Update CHANGELOG.md

0b51bd1

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

fix typo

36d0882

Merge pull request #262 from d4straub/dev

fda9e23

fix typo

d4straub merged commit e065754 into master Nov 26, 2021

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Release 2.1.1#261

Release 2.1.1#261
d4straub merged 74 commits into
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`nf-core lint` overall result: Passed ✅ ⚠️

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