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add dorado

Open yuukiiwa opened this issue 2 years ago • 1 comments

Currently, dorado v0.3.2 is incorporated into through its docker container. It works without demultiplexing, but doesn't work with demultiplexing with qcat downstream

I raised an issue on dorado's github repo requesting for the dorado v0.4.0 to be dockerized (here is the issue). Will not incorporate basecalling and demultiplexing until the dorado v0.4.0 is available on docker hub.

I made some changes to basecalling without demultiplexing, where the user can specify the input fast5 directory from the samplesheet for each sample. If a user has multiple sample, then he/she will have to indicate the respective input fast5 directory for those samples.

Here is the run on my machine: Screenshot from 2023-10-18 00-09-04

yuukiiwa avatar Oct 17 '23 09:10 yuukiiwa

nf-core lint overall result: Failed :x:

Posted for pipeline commit 5e61982

+| ✅ 215 tests passed       |+
!| ❗   6 tests had warnings |!
-| ❌  20 tests failed       |-

:x: Test failures:

  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/WorkflowNanoseq.groovy
  • nextflow_config - Config default value incorrect: params.kit is set as `` in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.flowcell is set as `` in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.dorado_model is set as `` in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.jaffal_ref_dir is set as for_jaffal in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.tracedir is set as ${params.outdir}/pipeline_info in nextflow_schema.json but is ./results/pipeline_info in nextflow.config.
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/email_template.html does not match the template
  • files_unchanged - assets/email_template.txt does not match the template
  • files_unchanged - assets/nf-core-nanoseq_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-nanoseq_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-nanoseq_logo_dark.png does not match the template
  • modules_config - conf/modules.config contains withName:STRINGTIE2, but the corresponding process is not present in any of the Nextflow scripts.

:heavy_exclamation_mark: Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.1.0
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • nfcore_yml - nf-core version not set in .nf-core.yml

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-26 05:37:20

github-actions[bot] avatar Oct 17 '23 16:10 github-actions[bot]

replaced by https://github.com/nf-core/nanoseq/pull/277

maxulysse avatar Oct 08 '24 05:10 maxulysse