Prevent rare error with sample sheet edge case

d4straub commented 1 year ago

Closes https://github.com/nf-core/ampliseq/issues/627

This PR attempts the fix by adding two sanity checks after reading the sample sheet that will raise a clear error with the request to change sampleIDs. I did think about fixing it in the problematic code line of the renaming module that picks up additionally to renamed files also an original input file, but I didn't come up with a feasible solution (all my solutions would require a re-factoring of multiple other modules to correct the sample ID).

Using the sample sheet samplesheet.tsv with content

sampleID    forwardReads    reverseReads
S127_02 S127_01.fastq.gz    S127_02.fastq.gz
S115    S115_1.fastq.gz S115_2.fastq.gz

with (1) nextflow run nf-core/ampliseq -r 2.6.1 -profile test,singularity --metadata false --input samplesheet.tsv --outdir results will fail with

ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC (S127_02)'

Caused by:
  Process `NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC (S127_02)` terminated with an error exit status (2)

Command executed:

  cutadapt \
      --cores 2 \
      --minimum-length 1 -O 3 -e 0.1 -g GTGYCAGCMGCCGCGGTAA -G GGACTACNVGGGTWTCTAAT --discard-untrimmed \
      -o S127_02.trimmed_1.trim.fastq.gz -p S127_02.trimmed_2.trim.fastq.gz \
      S127_02.fastq.gz S127_02_1.fastq.gz S127_02_2.fastq.gz \
      > S127_02.trimmed.cutadapt.log
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC":
      cutadapt: $(cutadapt --version)
  END_VERSIONS

Command exit status:
  2

Command output:
  (empty)

Command error:
  Run "cutadapt --help" to see command-line options.
  See https://cutadapt.readthedocs.io/ for full documentation.

  cutadapt: error: You provided 3 input file names, but either one or two are expected. The file names were:
   - 'S127_02.fastq.gz'
   - 'S127_02_1.fastq.gz'
   - 'S127_02_2.fastq.gz'
  Hint: If your path contains spaces, you need to enclose it in quotes

or (2) nextflow run nf-core/ampliseq -r 2.6.1 -profile test,singularity --metadata false --input samplesheet.tsv --outdir results --single_end will fail with:

ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC (S115)'

Caused by:
  Process `NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC (S115)` terminated with an error exit status (2)

Command executed:

  cutadapt \
      --cores 2 \
      --minimum-length 1 -O 3 -e 0.1 -g GTGYCAGCMGCCGCGGTAA --discard-untrimmed \
      -o S115.trimmed.trim.fastq.gz \
      S115.fastq.gz S115_1.fastq.gz \
      > S115.trimmed.cutadapt.log
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC":
      cutadapt: $(cutadapt --version)
  END_VERSIONS

Command exit status:
  2

Command output:
  (empty)

Command error:
  Run "cutadapt --help" to see command-line options.
  See https://cutadapt.readthedocs.io/ for full documentation.

  cutadapt: error: It appears you want to trim paired-end data because you provided two input files, but then you also need to provide two output files (with -o and -p) or use the --interleaved option.

PR checklist

[x] 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 - have you followed the pipeline conventions in the contribution docs
[ ] If necessary, also make a PR on the nf-core/ampliseq branch on the nf-core/test-datasets repository.
[x] Make sure your code lints (nf-core lint).
[x] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[x] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).

github-actions[bot] commented 1 year ago

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

Posted for pipeline commit 5a2b8cf

+| ✅ 152 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README did not have a Nextflow minimum version badge. * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Parameter `input` is not defined in the correct subschema (input_output_options) ### :grey_question: Tests ignored: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `conf/igenomes.config` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.gitattributes` * [actions_ci](https://nf-co.re/tools-docs/lint_tests/actions_ci.html) - actions_ci ### :white_check_mark: Tests passed: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitattributes` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitignore` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - 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`.gitignore` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.prettierignore` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `pyproject.toml` matches the template * [actions_awstest](https://nf-co.re/tools-docs/lint_tests/actions_awstest.html) - '.github/workflows/awstest.yml' is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools-docs/lint_tests/actions_awsfulltest.html) - `.github/workflows/awsfulltest.yml` is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools-docs/lint_tests/actions_awsfulltest.html) - `.github/workflows/awsfulltest.yml` does not use `-profile test` * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README Zenodo placeholder was replaced with DOI. * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - No TODO strings found * [pipeline_name_conventions](https://nf-co.re/tools-docs/lint_tests/pipeline_name_conventions.html) - Name adheres to nf-core convention * [template_strings](https://nf-co.re/tools-docs/lint_tests/template_strings.html) - Did not find any Jinja template strings (246 files) * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Schema lint passed * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Schema title + description lint passed * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Schema matched params returned from nextflow config * [system_exit](https://nf-co.re/tools-docs/lint_tests/system_exit.html) - No `System.exit` calls found * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: linting.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: awsfulltest.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: linting_comment.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: clean-up.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: awstest.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: fix-linting.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: ci.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: branch.yml * [merge_markers](https://nf-co.re/tools-docs/lint_tests/merge_markers.html) - No merge markers found in pipeline files * [modules_json](https://nf-co.re/tools-docs/lint_tests/modules_json.html) - Only installed modules found in `modules.json` * [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins. * [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains a matching 'report_comment'. * [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains 'export_plots: true'. * [modules_structure](https://nf-co.re/tools-docs/lint_tests/modules_structure.html) - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL' ### Run details * nf-core/tools version 2.9 * Run at `2023-08-29 13:15:45`

d4straub commented 1 year ago

Thanks!

nf-core / ampliseq