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@GallVp GallVp released this 05 Nov 20:18
2.2.0
0141925
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Learn about vigilant mode.

What's Changed

Added

  1. Added Gfastats #126
  2. Updated nf-core/template to 3.0.2 #149
  3. Updated samtools faidx to 1.21
  4. Now using nf-test for pipeline level testing #153
  5. Added text/html as content mime type for the report file #146
  6. Added a sequence labels table below the HiC contact map #147
  7. Added parameter hic_samtools_ext_args and set its default value to -F 3852 #159
  8. Added the HiC QC report to the final report so that users don't have to navigate to the results folder #162
  9. Added the fastp log to the final report #163
  10. Updated the tube map along with the tool list #166
  11. Added Orthofinder #167
  12. Changed order of tool options in the nextflow.config file
  13. Updated PFR's Kraken 2 database to k2_pluspfp_20240904 #170
  14. Increased memory requirement for Kraken 2 to 256.GB

Fixed

  1. Fixed a bug where Gene score distribution graph did not appear correctly #125
  2. Increased memory requirement for DNADIFF to avoid SLURM OOM kills with exit code 2 #141
  3. Documented the use explicit use of -revision parameter #160
  4. Now using _JAVA_OPTIONS in module RUNASSEMBLYVISUALIZER to avoid user preferences related errors

Dependencies

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

Deprecated

  1. Reduced the GenomeTools stats figures to 300 DPI #142
  2. Now synteny_mummer_min_bundle_size is set to 1000000 by default #142
  3. results is not the default output directory anymore
  4. Removed a number of unnecessary parameters: monochromeLogs, config_profile_contact, config_profile_url, validationFailUnrecognisedParams, validationLenientMode, validationSchemaIgnoreParams, validationShowHiddenParams validate_params
  5. Resource parameters have been removed: max_memory, max_cpus, max_time

Full Changelog: 2.1.1...2.2.0

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