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

Dsl2 annotation #386

Merged
merged 23 commits into from Jun 29, 2021
Merged

Dsl2 annotation #386

merged 23 commits into from Jun 29, 2021

Conversation

maxulysse
Copy link
Member

I'm starting to add annotation.

Based on the branch from #379, so git history should be fine once it's merged.

I think it make sense to have that as (a) separate subworkflow(s).

Already created the dockerhub images for snpeff/vep:
https://hub.docker.com/r/nfcore/snpeff
https://hub.docker.com/r/nfcore/vep

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/sarek 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).

@github-actions
Copy link

github-actions bot commented Jun 8, 2021 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b7781ea

+| ✅ 135 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗  82 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: environment.yml
  • files_exist - File not found: Dockerfile
  • nextflow_config - Config variable not found: process.container
  • params_used - Config variable not found in main.nf: params.input
  • params_used - Config variable not found in main.nf: params.step
  • params_used - Config variable not found in main.nf: params.genome
  • params_used - Config variable not found in main.nf: params.genomes_base
  • params_used - Config variable not found in main.nf: params.save_reference
  • params_used - Config variable not found in main.nf: params.help
  • params_used - Config variable not found in main.nf: params.no_intervals
  • params_used - Config variable not found in main.nf: params.nucleotides_per_second
  • params_used - Config variable not found in main.nf: params.sentieon
  • params_used - Config variable not found in main.nf: params.skip_qc
  • params_used - Config variable not found in main.nf: params.target_bed
  • params_used - Config variable not found in main.nf: params.tools
  • params_used - Config variable not found in main.nf: params.trim_fastq
  • params_used - Config variable not found in main.nf: params.clip_r1
  • params_used - Config variable not found in main.nf: params.clip_r2
  • params_used - Config variable not found in main.nf: params.three_prime_clip_r1
  • params_used - Config variable not found in main.nf: params.three_prime_clip_r2
  • params_used - Config variable not found in main.nf: params.trim_nextseq
  • params_used - Config variable not found in main.nf: params.save_trimmed
  • params_used - Config variable not found in main.nf: params.split_fastq
  • params_used - Config variable not found in main.nf: params.aligner
  • params_used - Config variable not found in main.nf: params.markdup_java_options
  • params_used - Config variable not found in main.nf: params.use_gatk_spark
  • params_used - Config variable not found in main.nf: params.save_bam_mapped
  • params_used - Config variable not found in main.nf: params.skip_markduplicates
  • params_used - Config variable not found in main.nf: params.ascat_ploidy
  • params_used - Config variable not found in main.nf: params.ascat_purity
  • params_used - Config variable not found in main.nf: params.cf_coeff
  • params_used - Config variable not found in main.nf: params.cf_contamination
  • params_used - Config variable not found in main.nf: params.cf_contamination_adjustment
  • params_used - Config variable not found in main.nf: params.cf_ploidy
  • params_used - Config variable not found in main.nf: params.cf_window
  • params_used - Config variable not found in main.nf: params.generate_gvcf
  • params_used - Config variable not found in main.nf: params.no_strelka_bp
  • params_used - Config variable not found in main.nf: params.pon
  • params_used - Config variable not found in main.nf: params.pon_index
  • params_used - Config variable not found in main.nf: params.ignore_soft_clipped_bases
  • params_used - Config variable not found in main.nf: params.umi
  • params_used - Config variable not found in main.nf: params.read_structure1
  • params_used - Config variable not found in main.nf: params.read_structure2
  • params_used - Config variable not found in main.nf: params.annotate_tools
  • params_used - Config variable not found in main.nf: params.annotation_cache
  • params_used - Config variable not found in main.nf: params.cadd_cache
  • params_used - Config variable not found in main.nf: params.cadd_indels
  • params_used - Config variable not found in main.nf: params.cadd_indels_tbi
  • params_used - Config variable not found in main.nf: params.cadd_wg_snvs
  • params_used - Config variable not found in main.nf: params.cadd_wg_snvs_tbi
  • params_used - Config variable not found in main.nf: params.genesplicer
  • params_used - Config variable not found in main.nf: params.snpeff_cache
  • params_used - Config variable not found in main.nf: params.config_profile_contact
  • params_used - Config variable not found in main.nf: params.config_profile_description
  • params_used - Config variable not found in main.nf: params.config_profile_url
  • params_used - Config variable not found in main.nf: params.outdir
  • params_used - Config variable not found in main.nf: params.publish_dir_mode
  • params_used - Config variable not found in main.nf: params.sequencing_center
  • params_used - Config variable not found in main.nf: params.multiqc_config
  • params_used - Config variable not found in main.nf: params.monochrome_logs
  • params_used - Config variable not found in main.nf: params.email
  • params_used - Config variable not found in main.nf: params.email_on_fail
  • params_used - Config variable not found in main.nf: params.plaintext_email
  • params_used - Config variable not found in main.nf: params.max_multiqc_email_size
  • params_used - Config variable not found in main.nf: params.hostnames
  • params_used - Config variable not found in main.nf: params.validate_params
  • params_used - Config variable not found in main.nf: params.tracedir
  • params_used - Config variable not found in main.nf: params.enable_conda
  • params_used - Config variable not found in main.nf: params.pull_docker_container
  • params_used - Config variable not found in main.nf: params.cpus
  • params_used - Config variable not found in main.nf: params.max_cpus
  • params_used - Config variable not found in main.nf: params.max_memory
  • params_used - Config variable not found in main.nf: params.max_time
  • actions_awsfulltest - .github/workflows/awsfulltest.yml should test full datasets, not -profile test
  • readme - README did not have a Nextflow minimum version badge.
  • pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable
  • pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in awstest.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • schema_description - No description provided in schema for parameter: cpus

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreSchema.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or foo
  • 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 1.14
  • Run at 2021-06-25 09:38:05

@maxulysse maxulysse mentioned this pull request Jun 11, 2021
Merged
11 tasks
@maxulysse
Copy link
Member Author

ok, now need to do something smart with the tag for the different images.
and need to figure out how to reuse a submodules while changing its parameters.

@maxulysse
Copy link
Member Author

and need to figure out how to reuse a submodules while changing its parameters.

Just need to spell the options properly actually...
🤦

@FriederikeHanssen
Copy link
Contributor

FriederikeHanssen commented Jun 23, 2021 •
edited

ok, now need to do something smart with the tag for the different images.

What do you mean here?

@maxulysse
Copy link
Member Author

ok, now need to do something smart with the tag for the different images.

What do you mean here?

Just did the commit B-)

@maxulysse maxulysse marked this pull request as ready for review June 23, 2021 12:31
@maxulysse
Copy link
Member Author

@KevinMenden @drpatelh can you check out this PR?

@drpatelh
Copy link
Member

Looks good to me guys. It would be much easier to see what is happening when these are submitted as separate nf-core/modules but otherwise 👌🏽 I have had to use customish modules for snpEff in viralrecon because I needed to create the db and run via the genome fasta and gff as opposed to an existing snpEff db. Be great to see these on nf-core modules though 💥

@maxulysse
Copy link
Member Author

Looks good to me guys. It would be much easier to see what is happening when these are submitted as separate nf-core/modules but otherwise 👌🏽 I have had to use customish modules for snpEff in viralrecon because I needed to create the db and run via the genome fasta and gff as opposed to an existing snpEff db. Be great to see these on nf-core modules though boom

Ok, then I start migrating modules to the nf-core/modules repo

@maxulysse maxulysse mentioned this pull request Jun 28, 2021
Merged
14 tasks
FriederikeHanssen
FriederikeHanssen approved these changes Jun 29, 2021
View reviewed changes
Copy link
Contributor

@FriederikeHanssen FriederikeHanssen left a comment

Choose a reason for hiding this comment

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

🚀

@maxulysse maxulysse merged commit 88ac395 into nf-core:dsl2 Jun 29, 2021
@maxulysse maxulysse deleted the dsl2_annotation branch June 29, 2021 14:02
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@KevinMenden KevinMenden Awaiting requested review from KevinMenden

@drpatelh drpatelh Awaiting requested review from drpatelh

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

Successfully merging this pull request may close these issues.

None yet
3 participants
@maxulysse @FriederikeHanssen @drpatelh