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@GallVp GallVp released this 21 Nov 07:46
0.5.0
ee702d7
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What's Changed

Added

  1. Added MultiQC #65
  2. Updated nf-core template to 3.0.2 #66
  3. Integrated nf-test into pipeline CI #68
  4. Updated the flowchart #87
  5. Added a large test dataset for the test_full profile #90
  6. Now .gff.gz and .gff3.gz inputs are also allowed for the benchmark column in --input
  7. Now removing liftoff genes with any intron shorted than 10bp #89
  8. Now also removing rRNA and tRNA after liftoff as the downstream logic in the pipeline can not correctly handle these
  9. Now skipping FastQC by default #98
  10. Added an HTML report #44
  11. Added content type as text/html for the MultiQC and genepal reports
  12. Added sra-tools for RNASeq data download #102

Fixed

  1. Now using ${meta.id}_trim as prefix for FASTQC files
  2. Updated citations to include DOIs
  3. Fixed a bug where FASTQ versions were not correctly captured
  4. Now using the correct out channel from STAR_ALIGN. This bug was introduced by a module update during the development of this version #74
  5. Fixed OrthoFinder results copy failure on AWS #108

Dependencies

  1. Nextflow!>=24.04.2
  2. [email protected]

Deprecated

  1. Resource parameters have been removed: max_memory, max_cpus, max_time
  2. Removed a number of unnecessary parameters: monochromeLogs, config_profile_contact, config_profile_url, validationFailUnrecognisedParams, validationLenientMode, validationSchemaIgnoreParams, validationShowHiddenParams, validate_params
  3. Removed extra_fastp_args and replaced it with fastp_extra_args
  4. Removed and replaced skip_fastp and skip_fastqc with fastp_skip and fastqc_skip #82

PRs

  • Updated nf-core template to 3.0.2 by @GallVp in #67
  • Integrated nf-test into pipeline CI by @GallVp in #71
  • Updated docs to include -r flag by @GallVp in #72
  • Now using the correct out channel from STAR_ALIGN by @GallVp in #78
  • Removed extra_fastp_args and replaced it with fastp_extra_args by @GallVp in #81
  • Removed and replaced skip_fastp and skip_fastqc by @GallVp in #83
  • Updated the flowchart by @GallVp in #88
  • Added a large dataset for test_full by @GallVp in #91
  • Now skipping FastQC by default by @GallVp in #99
  • Added an HTML report by @GallVp in #100
  • Added content type as text/html for the MultiQC and genepal reports by @GallVp in #101
  • Added sra-tools for RNASeq data download by @GallVp in #103
  • Fixed minor issues in report modules by @GallVp in #106
  • Fixed OrthoFinder results copy failure on AWS by @GallVp in #109
  • Added doi and bumped version by @GallVp in #110
  • Removed an unnecessary config block by @GallVp in #111
  • Fixed linting issues by @GallVp in #113
  • Added GeneMark license info by @GallVp in #114
  • Candidate for 0.5.0 by @GallVp in #112

Full Changelog: 0.4.0...0.5.0

Contributors

GallVp
Assets 2
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