8000 SL-117 fix featurecounts spec · Pull Request #27 · nf-core/rnasplice · GitHub
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SL-117 fix featurecounts spec #27

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Merged
1 commit merged into from
Nov 3, 2022
Merged

SL-117 fix featurecounts spec #27

1 commit merged into from
Nov 3, 2022

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ghost
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@ghost ghost commented Nov 3, 2022

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).

@ghost ghost merged commit 8052d98 into dev Nov 3, 2022
@ghost ghost deleted the SL-117-feature-counts-specification branch November 3, 2022 17:52
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github-actions bot commented Nov 3, 2022 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 12c070e

+| ✅ 156 tests passed       |+
!| ❗  11 tests had warnings |!
-| ❌  80 tests failed       |-

❌ Test failures:

  • schema_params - Param transcript_fasta from nextflow config not found in nextflow_schema.json
  • schema_params - Param additional_fasta from nextflow config not found in nextflow_schema.json
  • schema_params - Param gtf_extra_attributes from nextflow config not found in nextflow_schema.json
  • schema_params - Param gtf_group_features from nextflow config not found in nextflow_schema.json
  • schema_params - Param gencode from nextflow config not found in nextflow_schema.json
  • schema_params - Param save_reference from nextflow config not found in nextflow_schema.json
  • schema_params - Param min_trimmed_reads from nextflow config not found in nextflow_schema.json
  • schema_params - Param clip_r1 from nextflow config not found in nextflow_schema.json
  • schema_params - Param clip_r2 from nextflow config not found in nextflow_schema.json
  • schema_params - Param three_prime_clip_r1 from nextflow config not found in nextflow_schema.json
  • schema_params - Param three_prime_clip_r2 from nextflow config not found in nextflow_schema.json
  • schema_params - Param trim_nextseq from nextflow config not found in nextflow_schema.json
  • schema_params - Param save_trimmed from nextflow config not found in nextflow_schema.json
  • schema_params - Param skip_trimming from nextflow config not found in nextflow_schema.json
  • schema_params - Param skip_trimgalore_fastqc from nextflow config not found in nextflow_schema.json
  • schema_params - Param skip_fastqc from nextflow config not found in nextflow_schema.json
  • schema_params - Param skip_qc from nextflow config not found in nextflow_schema.json
  • schema_params - Param skip_bigwig from nextflow config not found in nextflow_schema.json
  • schema_params - Param aligner from nextflow config not found in nextflow_schema.json
  • schema_params - Param pseudo_aligner from nextflow config not found in nextflow_schema.json
  • schema_params - Param bam_csi_index from nextflow config not found in nextflow_schema.json
  • schema_params - Param seq_center from nextflow config not found in nextflow_schema.json
  • schema_params - Param salmon_quant_libtype from nextflow config not found in nextflow_schema.json
  • schema_params - Param star_ignore_sjdbgtf from nextflow config not found in nextflow_schema.json
  • schema_params - Param skip_alignment from nextflow config not found in nextflow_schema.json
  • schema_params - Param save_unaligned from nextflow config not found in nextflow_schema.json
  • schema_params - Param save_align_intermeds from nextflow config not found in nextflow_schema.json
  • schema_params - Param save_merged_fastq from nextflow config not found in nextflow_schema.json
  • schema_params - Param rmats from nextflow config not found in nextflow_schema.json
  • schema_params - Param rmats_splice_diff_cutoff from nextflow config not found in nextflow_schema.json
  • schema_params - Param rmats_paired_stats from nextflow config not found in nextflow_schema.json
  • schema_params - Param rmats_read_len from nextflow config not found in nextflow_schema.json
  • schema_params - Param rmats_novel_splice_site from nextflow config not found in nextflow_schema.json
  • schema_params - Param rmats_min_intron_len from nextflow config not found in nextflow_schema.json
  • schema_params - Param rmats_max_exon_len from nextflow config not found in nextflow_schema.json
  • schema_params - Param dexseq_exon from nextflow config not found in nextflow_schema.json
  • schema_params - Param gff_dexseq from nextflow config not found in nextflow_schema.json
  • schema_params - Param alignment_quality from nextflow config not found in nextflow_schema.json
  • schema_params - Param aggregation from nextflow config not found in nextflow_schema.json
  • schema_params - Param deu_lfc_denominator from nextflow config not found in nextflow_schema.json
  • schema_params - Param edger_exon from nextflow config not found in nextflow_schema.json
  • schema_params - Param dexseq_dtu from nextflow config not found in nextflow_schema.json
  • schema_params - Param dtu_txi from nextflow config not found in nextflow_schema.json
  • schema_params - Param dtu_lfc_denominator from nextflow config not found in nextflow_schema.json
  • schema_params - Param min_samps_feature_expr from nextflow config not found in nextflow_schema.json
  • schema_params - Param min_samps_feature_prop from nextflow config not found in nextflow_schema.json
  • schema_params - Param min_samps_gene_expr from nextflow config not found in nextflow_schema.json
  • schema_params - Param min_feature_expr from nextflow config not found in nextflow_schema.json
  • schema_params - Param min_feature_prop from nextflow config not found in nextflow_schema.json
  • schema_params - Param min_gene_expr from nextflow config not found in nextflow_schema.json
  • schema_params - Param suppa from nextflow config not found in nextflow_schema.json
  • schema_params - Param suppa_per_local_event from nextflow config not found in nextflow_schema.json
  • schema_params - Param suppa_per_isoform from nextflow config not found in nextflow_schema.json
  • schema_params - Param local_events from nextflow config not found in nextflow_schema.json
  • schema_params - Param pool_genes from nextflow config not found in nextflow_schema.json
  • schema_params - Param suppa_tpm from nextflow config not found in nextflow_schema.json
  • schema_params - Param diffsplice_local_event from nextflow config not found in nextflow_schema.json
  • schema_params - Param diffsplice_isoform from nextflow config not found in nextflow_schema.json
  • schema_params - Param diffsplice_method from nextflow config not found in nextflow_schema.json
  • schema_params - Param diffsplice_area from nextflow config not found in nextflow_schema.json
  • schema_params - Param diffsplice_lower_bound from nextflow config not found in nextflow_schema.json
  • schema_params - Param diffsplice_gene_correction from nextflow config not found in nextflow_schema.json
  • schema_params - Param diffsplice_paired from nextflow config not found in nextflow_schema.json
  • schema_params - Param diffsplice_alpha from nextflow config not found in nextflow_schema.json
  • schema_params - Param diffsplice_median from nextflow config not found in nextflow_schema.json
  • schema_params - Param diffsplice_tpm_threshold from nextflow config not found in nextflow_schema.json
  • schema_params - Param diffsplice_nan_threshold from nextflow config not found in nextflow_schema.json
  • schema_params - Param clusterevents_local_event from nextflow config not found in nextflow_schema.json
  • schema_params - Param clusterevents_isoform from nextflow config not found in nextflow_schema.json
  • schema_params - Param clusterevents_sigthreshold from nextflow config not found in nextflow_schema.json
  • schema_params - Param clusterevents_dpsithreshold from nextflow config not found in nextflow_schema.json
  • schema_params - Param clusterevents_eps from nextflow config not found in nextflow_schema.json
  • schema_params - Param clusterevents_metric from nextflow config not found in nextflow_schema.json
  • schema_params - Param clusterevents_separation from nextflow config not found in nextflow_schema.json
  • schema_params - Param clusterevents_min_pts from nextflow config not found in nextflow_schema.json
  • schema_params - Param clusterevents_method from nextflow config not found in nextflow_schema.json
  • schema_params - Param gtf from nextflow config not found in nextflow_schema.json
  • schema_params - Param gff from nextflow config not found in nextflow_schema.json
  • schema_params - Param star_index from nextflow config not found in nextflow_schema.json
  • schema_params - Param salmon_index from nextflow config not found in nextflow_schema.json

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in README.md: Write a 1-2 sentence summary of what data the pipeline is for and what it does
  • 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: Fill in short bullet-pointed list of the default steps in 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-11-03 17:53:37

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