8000 fix samplesheet location by jma1991 · Pull Request #40 · nf-core/rnasplice · GitHub
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fix samplesheet location #40

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Merged
merged 1 commit into from
Feb 17, 2023
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jma1991
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@jma1991 jma1991 commented Feb 17, 2023

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 - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/rnasplice 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 --outdir <OUTDIR>).
  • 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).

@jma1991 jma1991 requested a review from bensouthgate February 17, 2023 09:47
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github-actions bot commented Feb 17, 2023

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 602f90c

+| ✅ 157 tests passed       |+
!| ❗  63 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: Update the example "typical command" below used to run the pipeline
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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
  • schema_description - No description provided in schema for parameter: gff
  • schema_description - No description provided in schema for parameter: rmats
  • schema_description - No description provided in schema for parameter: rmats_splice_diff_cutoff
  • schema_description - No description provided in schema for parameter: rmats_paired_stats
  • schema_description - No description provided in schema for parameter: rmats_read_len
  • schema_description - No description provided in schema for parameter: rmats_novel_splice_site
  • schema_description - No description provided in schema for parameter: rmats_min_intron_len
  • schema_description - No description provided in schema for parameter: rmats_max_exon_len
  • schema_description - No description provided in schema for parameter: dexseq_exon
  • schema_description - No description provided in schema for parameter: save_dexseq_annotation
  • schema_description - No description provided in schema for parameter: gff_dexseq
  • schema_description - No description provided in schema for parameter: alignment_quality
  • schema_description - No description provided in schema for parameter: aggregation
  • schema_description - No description provided in schema for parameter: deu_lfc_denominator
  • schema_description - No description provided in schema for parameter: edger_exon
  • schema_description - No description provided in schema for parameter: dexseq_dtu
  • schema_description - No description provided in schema for parameter: dtu_txi
  • schema_description - No description provided in schema for parameter: dtu_lfc_denominator
  • schema_description - No description provided in schema for parameter: min_samps_feature_expr
  • schema_description - No description provided in schema for parameter: min_samps_feature_prop
  • schema_description - No description provided in schema for parameter: min_samps_gene_expr
  • schema_description - No description provided in schema for parameter: min_feature_expr
  • schema_description - No description provided in schema for parameter: min_feature_prop
  • schema_description - No description provided in schema for parameter: min_gene_expr
  • schema_description - No description provided in schema for parameter: suppa
  • schema_description - No description provided in schema for parameter: suppa_per_local_event
  • schema_description - No description provided in schema for parameter: suppa_per_isoform
  • schema_description - No description provided in schema for parameter: suppa_tpm
  • schema_description - No description provided in schema for parameter: generateevents_pool_genes
  • schema_description - No description provided in schema for parameter: generateevents_localevents
  • schema_description - No description provided in schema for parameter: generateevents_boundary
  • schema_description - No description provided in schema for parameter: generateevents_threshold
  • schema_description - No description provided in schema for parameter: generateevents_exon_length
  • schema_description - No description provided in schema for parameter: psiperevent_total_filter
  • schema_description - No description provided in schema for parameter: diffsplice_local_event
  • schema_description - No description provided in schema for parameter: diffsplice_isoform
  • schema_description - No description provided in schema for parameter: diffsplice_method
  • schema_description - No description provided in schema for parameter: diffsplice_area
  • schema_description - No description provided in schema for parameter: diffsplice_lower_bound
  • schema_description - No description provided in schema for parameter: diffsplice_gene_correction
  • schema_description - No description provided in schema for parameter: diffsplice_paired
  • schema_description - No description provided in schema for parameter: diffsplice_alpha
  • schema_description - No description provided in schema for parameter: diffsplice_median
  • schema_description - No description provided in schema for parameter: diffsplice_tpm_threshold
  • schema_description - No description provided in schema for parameter: diffsplice_nan_threshold
  • schema_description - No description provided in schema for parameter: clusterevents_local_event
  • schema_description - No description provided in schema for parameter: clusterevents_isoform
  • schema_description - No description provided in schema for parameter: clusterevents_sigthreshold
  • schema_description - No description provided in schema for parameter: clusterevents_dpsithreshold
  • schema_description - No description provided in schema for parameter: clusterevents_eps
  • schema_description - No description provided in schema for parameter: clusterevents_metric
  • schema_description - No description provided in schema for parameter: clusterevents_separation
  • schema_description - No description provided in schema for parameter: clusterevents_min_pts
  • schema_description - No description provided in schema for parameter: clusterevents_method

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-02-17 09:49:03

@bensouthgate bensouthgate merged commit b716990 into nf-core:dev Feb 17, 2023
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Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

@jma1991 jma1991 deleted the fix_samplesheet branch February 22, 2023 13:55
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