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Releases: Plant-Food-Research-Open/assemblyqc

Version 2.1.1

19 Sep 22:52
@GallVp GallVp
2.1.1
cec2728
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Version 2.1.1 Latest
Latest

What's Changed

  • Made the hic param pattern more flexible by @GallVp in #131
  • Updated modules to remove Bioconda defaults channel by @GallVp in #133
  • Fixed flowchart syntax to remove '\n' by @GallVp in #134
  • Now correctly validating gff files for circular sequences by @GallVp in #136
  • Version bump to 2.1.1 by @GallVp in #137
  • Formatted mermaid chart by @GallVp in #138
  • Fixed the branch protection GitHub action by @GallVp in #140
  • Candidate for 2.1.1 by @GallVp in #139

Full Changelog: 2.1.0...2.1.1

Contributors

GallVp
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Version 2.1.0

02 Aug 01:33
@GallVp GallVp
2.1.0
d1c2f0a
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Version 2.1.0

What's Changed

Full Changelog: 2.0.0...2.1.0

Added

  1. Created summary presence/absence tables for NCBI FCS modules #88
  2. Added min. system requirements #91
  3. Added a test to verify the fix for the bug which resulted in a pipeline crash for assemblies without LTRs
  4. Updated NCBI FCS GX to 0.5.4 #93
  5. Updated SYRI to 1.7.0 #104
  6. Added a script to automatically check for updates on GitHub/GitLab and post issues
  7. Updated modules: UNTAR, MERYL_COUNT, GUNZIP, MINIMAP2_ALIGN, FASTQC

Fixed

  1. Fixed a bug where intron_length_distribution was used instead of cds_length_distribution when creating the CDS Length Distribution Graph #95
  2. Fixed a bug where 'Subsequent pipeline modules are skipped.' was printed in the report.html even when contamination_stops_pipeline was set to false
  3. Now NCBI FCS GX module uses all the cores available from the Nextflow task
  4. Fixed a bug which caused PLOTSR to fail for certain assembly names #102
  5. Now LTRRETRIEVER_LTRRETRIEVER does not crash when the input assembly does not contain any LTRs #92
  6. Now LTRRETRIEVER_LTRRETRIEVER does not crash when the input assembly is not writable #98
  7. Now soft masked regions are unmasked before computing LAI #117
  8. Fixed a bug in ASSEMBLATHON_STATS which caused it to fail on MMC executor due to multiple binds of the bin directory
  9. Changed NextFlow to Nextflow
  10. Updated citation to Bioinformatics

Dependencies

  1. Nextflow!>=23.04.0
  2. [email protected]

Deprecated

  1. Changed default branch name from master to main in nf-core template files
  2. Moved version_check.sh to .github/version_checks.sh
  3. Moved docs/contributors.sh to .github/contributors.sh
  4. Removed dependency on https://github.com/PlantandFoodResearch/nxf-modules.git
  5. Replaced nf-core/fastq_trim_fastp_fastqc with nf-core/fastq_fastqc_umitools_fastp which has nf-test unit tests
  6. Removed version check on README.md
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Version 2.0.0

05 Jun 07:47
@GallVp GallVp
2.0.0
690e56b
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Version 2.0.0

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. [email protected]

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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Version 1.4

04 Mar 01:56
@GallVp GallVp
1.4
9dfb828
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Version 1.4

What's Changed

Added

  1. Now it is possible to skip FASTP and FASTQC for the HIC module
  2. Renamed ASSEMBLY_QC workflow to ASSEMBLYQC
  3. Now using nf-core/FASTA_EXPLORE_SEARCH_PLOT_TIDK
  4. Now redirecting validation errors to AssemblyQC report
  5. Simplified layout of CITATIONS.md file
  6. Now using pfr/gff3_validate sub-workflow for gff3 validation
  7. Now listing software versions from the versions.yml file
  8. Replaced custom GUNZIP module with nf-core/gunzip
  9. Replaced custom gt/stat with pfr/gt/stat
  10. Replaced custom fasta_validator with nf-core/fastavalidator
  11. Added pre-commit version checking
  12. Now gt/stat reports extended stats and multiple distribution plots have been added to the report
  13. Added a tools tab to the report which lists the tools used by the pipeline to create the report
  14. Refactored and cleaned data flows for all the custom sub-workflow
  15. Started using nf-core template
  16. Started using semantic versioning
  17. Moved all python depending packages to 'docker.io/gallvp/python3npkgs:v0.6'

Fixed

  1. All modules are now emitting versioning information
  2. Fixed a bug which caused LAI to run with null assembly fasta
  3. Fixed FASTA_LTRRETRIEVER_LAI sub-workflow so that it respects monoploid_ids parameter.

Dependencies

  1. NextFlow!>=23.04.0
  2. [email protected]

Deprecated

  1. Removed BIOCODE GFF3 STATS owing to its frequent failures
Assets 2
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