Skip to content
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

Switch to DSL2 #171

Merged
merged 68 commits into from
Mar 23, 2021
Merged

Switch to DSL2 #171

merged 68 commits into from
Mar 23, 2021

Conversation

skrakau
Copy link
Member

@skrakau skrakau commented Mar 23, 2021

Basically containing only PR #162.

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 - add to the software_versions process and a regex to scrape_software_versions.py
  • 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 March 18, 2021 11:16
@skrakau
First dsl2 draft
656c04f
@skrakau
Replace 'input_paths' param by 'input'
04d8698
@skrakau
Fix metabat2 input channel
687fe5a
@skrakau
Revert to preevious input check (without python script)
eb8899c
@skrakau
Reordered sections in main.nf
e76a612
@skrakau
Fix help command
3e8c311
@skrakau
Adjust base.config to new process names
7663a28
@skrakau
Delete undefined and unused parameter
436d8fd
@skrakau
Delete unused genome parameter checks
950aac7
@skrakau
Removed docker parts from GitHub actions files
beff220
@skrakau
Whitespace
6fb3cdd
@skrakau
Apply manually remaining changes from recent dev commits
1d864a2
@skrakau
Fix augustus_config_path used in busco process
b431e45
@skrakau
Update busco biocontainer version to fix singularity issue
dca759b
@skrakau
Update krona to new biocontainer build to fix download issue with sin…
c7957f8 
…gularity
@skrakau
Completed collection of software versions
af3e040
@skrakau
Replace input/output type 'file' by 'path'
2d3284b
@skrakau
Removed comment
a0eea20
@skrakau
Create subworkflow for busco processes
2cd6014
@skrakau
Create subworkflow for binning with MetaBAT2
d9d6f20
@skrakau
Restructured grouping and pooling for assemlby code
5300d09
@skrakau
Renamed busco subworkflow
22a3c83
@skrakau
Change fastqc output file type
ad10c5a
@skrakau
Adjust publish folder structure
bdb26c5
@skrakau
Fix busco db usage
e8272f4
@skrakau
Remove publishDir for bowite2_index
6c4a84a
@skrakau
Removed bowtie nf-core module
c2f7f64
@skrakau
Fix content for ch_bowtie2_assembly_multiqc channel again
5c831eb
@skrakau
Cleaned up meta and related fields
8c7fd57
@skrakau
Fix overwritting of meta map items by using clone()
8949803
skrakau and others added 23 commits March 18, 2021 11:18
@skrakau
Remove def in front of options to enable -resume
42d3982
@skrakau
Removed 'RENAME_FASTQS' process (done by fastqc and fastp)
32270fe
@skrakau
Use consistent naming for paired-end reads (_1/2)
11fe163
@skrakau
Update cat and diamond container, fix mv of files
8c9b51e
@skrakau
Turn on publish_by_id for CAT
84b3848
@skrakau
Update required nextflowVersion to >=20.10.0
5ad62c6
@skrakau
Add container (biocontainers:v1.2.0_cv1) for processes still without
728df22
@skrakau
Fix nextflow version for badge and ci test
289bae6
@skrakau
Update schema for fastp params
00aae98
@skrakau
Add changes for nf-core tools 1.13
515798e
@skrakau
Update .github/workflows/branch.yml for tools 1.13.1
b8db1ee
@skrakau
Remove addParams( options: [:] )
ef415f7
@skrakau
Renamed CustomSchema.groovy to MagUtils.groovy
0b265a9
@skrakau
Add software version to KRONA_DB module
f1d5df3
@skrakau
Add software version to BUSCO_PLOT module
ed885c4
@skrakau
Add missing emits
bc54d57
@skrakau
Move samplesheet parsing to subworkflow
6822d86
@skrakau
Adjust beginning of assets/multiqc_config.yaml to template
62baec2
@skrakau
Do not list removed param 'manifest' as deprecated anymore
e33b556
@skrakau
Adjust default param values to types to cleanup summary
e76c2fe
@skrakau
Use -1 as default for *_fix_cpus int params
303a3c2
@skrakau
Parallellise CI tests for profiles
b9f220e
@skrakau
Merge pull request #162 from skrakau/dsl2_first_draft
ecab713 
Dsl2 first draft
@skrakau skrakau requested a review from d4straub March 23, 2021 12:43
d4straub
d4straub approved these changes Mar 23, 2021
View reviewed changes
Copy link
Collaborator

@d4straub d4straub left a comment •
edited
Loading

Choose a reason for hiding this comment

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

Looks great!

@github-actions
Copy link

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ecab713

+| ✅ 116 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   4 tests had warnings |!
### ❗ Test warnings:

❔ Tests ignored:

  • files_unchanged - File does not exist: .github/workflows/push_dockerhub_dev.yml
  • files_unchanged - File does not exist: .github/workflows/push_dockerhub_release.yml
  • conda_env_yaml - No environment.yml file found - skipping conda_env_yaml test
  • conda_dockerfile - No environment.yml / Dockerfile file found - skipping conda_dockerfile test

✅ Tests passed:

Run details

  • nf-core/tools version 1.13.1
  • Run at 2021-03-23 12:45:53

@skrakau
Copy link
Member Author

skrakau commented Mar 23, 2021

Thanks @d4straub

@skrakau skrakau merged commit 4ce64ff into dev Mar 23, 2021
@skrakau skrakau mentioned this pull request Mar 23, 2021
Closed
@jfy133 jfy133 deleted the dsl2 branch March 14, 2023 09:07
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@d4straub d4straub d4straub 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.
2 participants
@skrakau @d4straub