Version 2.2.0

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

Version 2.1.1

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

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

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

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