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 fixes #390

Merged
merged 8 commits into from
Jun 18, 2021
Merged

Dsl2 fixes #390

merged 8 commits into from
Jun 18, 2021

Conversation

maxulysse
Copy link
Member

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 17, 2021 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 06d9585

+| ✅ 134 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 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 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 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 2021-06-18 07:40:41

ewels
ewels approved these changes Jun 17, 2021
View reviewed changes
Copy link
Member

@ewels ewels left a comment

Choose a reason for hiding this comment

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

Looks great!

nextflow_schema.json Outdated Show resolved Hide resolved
@maxulysse @ewels
Update nextflow_schema.json
06d9585 
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
@maxulysse maxulysse merged commit df65564 into nf-core:dsl2 Jun 18, 2021
@maxulysse maxulysse deleted the dsl2_fixes branch June 18, 2021 07:54
@maxulysse maxulysse mentioned this pull request Jun 21, 2021
Merged
11 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@ewels ewels ewels 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
@maxulysse @ewels