8000 Release 2.1.1 by d4straub · Pull Request #261 · nf-core/mag · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

Release 2.1.1 #261

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
merged 74 commits into from
Nov 26, 2021
Merged

Release 2.1.1 #261

merged 74 commits into from
Nov 26, 2021

Conversation

d4straub
Copy link
Collaborator
@d4straub d4straub commented Nov 23, 2021 •
edited
Loading

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

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
    • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
    • If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repository.
  • 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).

skrakau and others added 30 commits July 29, 2021 15:45
@skrakau
Bump version 2.2.0dev and adjusted release date
b1e5242
@skrakau
Merge pull request #228 from skrakau/bump_2.2.0dev
d4335b1 
Bump version 2.2.0dev and adjusted release date
@jfy133
Add correct CC-BY attribution to workflow diagram
3a39e40
@d4straub
fix large assemblies
4fdc450
@d4straub
fix typo
bf0439f
@d4straub
Merge pull request #231 from jfy133/master
6970953 
Fix workflow diagram CC-BY attribution
@d4straub
fix centrifuge error
b49357d
@d4straub
Merge pull request #236 from d4straub/dev
d63ce61 
fix large assemblies
@AntoniaSchuster
Added nf-core/modules/prodigal
cb64b22
@AntoniaSchuster
citations, docs and small changes
8b1b288
@AntoniaSchuster
Update README and CHANGELOG
adab749
@AntoniaSchuster
Remove trailing whitespaces
2daeae0
@AntoniaSchuster @d4straub
Update CHANGELOG.md
3799d02 
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
@AntoniaSchuster @d4straub
Update docs/output.md
f619652 
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
@AntoniaSchuster
Updated output, changed prodigal options so predictions for different…
6825bd0 
… assemblers are not overwritten.
@AntoniaSchuster
Merge branch 'dev' of https://github.com/AntoniaSchuster/mag into dev
5d0103a
@AntoniaSchuster
update prodigal citation
9b7ad0c
@AntoniaSchuster
Merge pull request #240 from AntoniaSchuster/dev
bf83c44 
Add Prodigal
@AntoniaSchuster
Implement skip_prodigal
1b70241
@AntoniaSchuster
Update schema
3d43755
@AntoniaSchuster
Update CHANGELOG.md
e6ab3de
@AntoniaSchuster
Remove trailing whitespaces
8694f53
@AntoniaSchuster @d4straub
Update CHANGELOG.md
4df589b 
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
@AntoniaSchuster @d4straub
Update nextflow.config
deb8358 
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
@AntoniaSchuster
Merge pull request #241 from AntoniaSchuster/skip_prodigal
554caee 
Add --skip_prodigal
@d4straub
add preprint info
61411b6
@AntoniaSchuster
nf-core modules install prokka
2646966
@d4straub
fix PR no
73827c3
@d4straub @AntoniaSchuster
Update CHANGELOG.md
17a0770 
Co-authored-by: AntoniaSchuster <56543138+AntoniaSchuster@users.noreply.github.com>
@AntoniaSchuster
Add prokka
d59c144
d4straub and others added 19 commits November 22, 2021 12:16
@d4straub
update changelog
5c511e1
@d4straub
fix channel
82a1c86
@d4straub
update changelog
b131da1
@d4straub
Merge branch 'dev' of https://github.com/nf-core/mag into fix-skip_busco
7f6bc44
@d4straub
fix update changelog
2db3c2d
@d4straub
Merge branch 'dev' of https://github.com/nf-core/mag into update-gtdb…
1cf290b 
…tk-conda
@d4straub
Merge pull request #255 from d4straub/update-gtdbtk-conda
1e98dd2 
fix gtdbtk conda channel
@d4straub
add fastp results to MultiQC
da0a283
@d4straub
speed up test_busco_auto by skipping some steps
b9175dd
@d4straub
fix typo
1bc7d0e
@d4straub
Merge pull request #258 from d4straub/add-fastp-to-multiqc
abe85c9 
Add fastp to multiqc
@d4straub
merge upstream
a7f7e9d
@d4straub
change gtdb default to mirror
a9399df
@d4straub @ggabernet
Update lib/WorkflowMag.groovy
b45414b 
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
@d4straub
Merge pull request #256 from d4straub/fix-skip_busco
2caec7c 
Fix --skip_busco
@d4straub
update SPAdes and MEGAHIT
f405bed
@d4straub
bump version
42ffda6
@d4straub
unify indent
70029fa
@d4straub
Merge pull request #260 from d4straub/dev
8000
5a74dba 
Prepare for release 2.1.1
@github-actions
Copy link
github-actions bot commented Nov 23, 2021 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fda9e23

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

❗ 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:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-11-25 12:03:02

ggabernet
ggabernet approved these changes Nov 25, 2021
View reviewed changes
Copy link
Member
@ggabernet ggabernet left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks good to me!

jfy133
jfy133 approved these changes Nov 25, 2021
View reviewed changes
Copy link
Member
@jfy133 jfy133 left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM 👍

@d4straub @jfy133
Update CHANGELOG.md
0b51bd1 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@d4straub
Copy link
Collaborator Author

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
Copy link
Member
jfy133 commented Nov 25, 2021 •
edited
Loading

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

mag/lib/WorkflowMag.groovy

Lines 83 to 119 in 0b51bd1

FB77
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
Copy link
Collaborator Author

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

@jfy133
Copy link
Member
jfy133 commented Nov 25, 2021

Approved

@d4straub d4straub merged commit e065754 into master Nov 26, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@ggabernet ggabernet ggabernet approved these changes

@jfy133 jfy133 jfy133 approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
5 participants
@d4straub @jfy133 @ggabernet @skrakau @AntoniaSchuster
0