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Dsl2 annotation #386

Merged
merged 23 commits into from
Jun 29, 2021
Merged

Dsl2 annotation #386

merged 23 commits into from
Jun 29, 2021

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maxulysse
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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).

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github-actions bot commented Jun 8, 2021 •
edited
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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
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@maxulysse
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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
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and need to figure out how to reuse a submodules while changing its parameters.

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

@FriederikeHanssen
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FriederikeHanssen commented Jun 23, 2021 •
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ok, now need to do something smart with the tag for the different images.

What do you mean here?

@maxulysse
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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
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@KevinMenden @drpatelh can you check out this PR?

@drpatelh
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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
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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
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FriederikeHanssen
FriederikeHanssen approved these changes Jun 29, 2021
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🚀

@maxulysse maxulysse merged commit 88ac395 into nf-core:dsl2 Jun 29, 2021
@maxulysse maxulysse deleted the dsl2_annotation branch June 29, 2021 14:02
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@KevinMenden KevinMenden Awaiting requested review from KevinMenden

@drpatelh drpatelh Awaiting requested review from drpatelh

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@maxulysse @FriederikeHanssen @drpatelh