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Published 20 hours ago • verified publisher icon nf-core

Sample IDs should work without underscores

Open edmundmiller opened this issue 1 year ago • 5 comments
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Closes #158

@dmitrymyl just made a test case for now, it passed so I'm not sure where the bug is.

Could you try your full run on the dev branch?

edmundmiller avatar Aug 17 '24 03:08 edmundmiller

nf-core lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit d1c51a0

+| ✅ 199 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   2 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

  • 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 preferred methods description, e.g. add publication citation for this pipeline

:grey_question: Tests ignored:

  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • actions_ci - actions_ci

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-17 16:14:57

github-actions[bot] avatar Aug 17 '24 03:08 github-actions[bot]

I ran the pipeline dev version with samplesheet:

sample,fastq_1,fastq_2
REP1,./sortmerna/SRR1693611/out/other.fq.gz,
REP2,./sortmerna/SRR1693612/out/other.fq.gz,

The sample names are different in this case, since I cannot run latest version with the same sample name. It failed with:

ERROR ~ Error executing process > 'NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:GROHMM:GROHMM_PARAMETERTUNING (REP2)'

Caused by:
  No such variable: bam -- Check script '/users/dmitry.mylarshchikov/.nextflow/assets/nf-core/nascent/./workflows/../subworkflows/local/./grohmm/../../../modules/local/grohmm/parametertuning/main.nf' at line: 26

Source block:
  def args = task.ext.args ?: ''
  def prefix = task.ext.prefix ?: "${meta.id}"
  """
      parameter_tuning.R \\
          --bam_file ${bam} \\
          --tuning_file ${tune_parameter_file} \\
          --outprefix ${prefix} \\
          --gtf $gtf \\
          --outdir ./ \\
          --cores $task.cpus \\
          $args

      cat <<-END_VERSIONS > versions.yml
      "${task.process}":
          r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
          bioconductor-grohmm: \$(Rscript -e "library(groHMM); cat(as.character(packageVersion('groHMM')))")
      END_VERSIONS
      """

dmitrymyl avatar Aug 19 '24 13:08 dmitrymyl

Okay, that's out of bounds 😆

sample,fastq_1,fastq_2
replicate1,./sortmerna/SRR1693611/out/other.fq.gz,
replicate2,./sortmerna/SRR1693612/out/other.fq.gz,

Maybe?

Might be able to improve the error handling earlier in the pipeline with nf-schema to abort if is a name is just REP1

edmundmiller avatar Aug 22 '24 01:08 edmundmiller

I renamed samples to "replicate1" and "replicate2", and I still get the same error from GROHMM_PARAMETERTUNING.

dmitrymyl avatar Aug 30 '24 11:08 dmitrymyl

Small bump on this PR (spring cleaning)! @edmundmiller Maybe this can be closed?

famosab avatar Mar 10 '25 14:03 famosab