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@GallVp GallVp released this 05 Jun 07:47
· 160 commits to main since this release
2.0.0
690e56b
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What's Changed

Full Changelog: 1.4...2.0.0

Added

  1. Updated nf-core/template to 2.14.1
  2. Removed release-announcements GitHub workflow
  3. Added a list of nf-core contributors
  4. Added a launcher script for local testing local_assemblyqc
  5. Added a custom BUNDLELINKS module which respects direction when bundling DNADIFF links #82
  6. Added the ability to create linear synteny plot in addition to the circos plot #74
  7. Updated modules and sub-workflows: BWA/INDEX, BWA/MEM, CAT/CAT, , CUSTOM/RESTOREGFFIDS, CUSTOM/SHORTENFASTAIDS, GT/GFF3, GT/GFF3VALIDATOR, GT/STAT, LTRFINDER, LTRHARVEST, LTRRETRIEVER/LAI, LTRRETRIEVER/LTRRETRIEVER, SAMBLASTER, FASTA_LTRRETRIEVER_LAI, FASTQ_BWA_MEM_SAMBLASTER, GFF3_VALIDATE, CUSTOM/SRATOOLSNCBISETTINGS, FASTP, FASTQC, UNTAR, SEQKIT/SEQ, SEQKIT/SORT, FASTA_EXPLORE_SEARCH_PLOT_TIDK
  8. Now the contamination_stops_pipeline flag allows the pipeline to continue if contamination is detected. It's default value is true #54
  9. Now fasta ids are sorted in natural order for the HiC module #76
  10. Now using FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS for SRA downloads
  11. Added MERQURY module #85
  12. Replaced GFF3_VALIDATE sub-workflow with GFF3_GT_GFF3_GFF3VALIDATOR_STAT
  13. Replaced local BUSCO module with FASTA_GXF_BUSCO_PLOT sub-workflow #75
  14. Replaced local NCBI_FCS_ADAPTOR with nf-core module and updated to 0.5.0 which includes additional adaptors for PacBio and Nanopore technologies #55
  15. Added PLOTSR #77
  16. Added JADWOS01 assembly to xrefsheet for successfully running PLOTSR
  17. Now detecting duplicate sequences with SEQKIT/RMDUP #64

Fixed

  1. Fixed a bug which caused NCBI_FCS_GX to not resume #80
  2. Restored the original version of nf-core/subworkflows/fastq_trim_fastp_fastqc
  3. Fixed n-core linting
  4. Updated tower.yml
  5. Updated LICENSE copyright to Copyright (c) 2024 The New Zealand Institute for Plant and Food Research Limited #81
  6. RUNASSEMBLYVISUALIZER is now single threaded for successful execution on both Linux and MacOS
  7. Fixed java memory overflow issues in RUNASSEMBLYVISUALIZER
  8. Updated FASTA_LTRRETRIEVER_LAI to fix a pipeline crash when ch_monoploid_seqs was [ meta, [] ] #83
  9. Improved input assembly documentation #86
  10. Added assembly tag to synteny warning message regarding missing synteny_labels file
  11. Now copying files in NCBI_FCS_GX_SETUP_SAMPLE rather than symlinking in an attempt to support NextFlow Fusion

Dependencies

  1. NextFlow!>=23.04.0
  2. nf-validation@1.1.3

Deprecated

  1. Removed CIRCOS_BUNDLELINKS module
  2. Now the default value of synteny_plot_1_vs_all is false
  3. Replace module CUSTOM/CHECKGFF3FASTACORRESPONDENCE with a local groovy function in GFF3_GT_GFF3_GFF3VALIDATOR_STAT sub-workflow
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