v3.0.0

What's Changed

• Round memory down for SPAdes by @gregorysprenger in #88
• Add SKESA parameters to main params.config by @gregorysprenger in #90
• Refactor profiles for use in Seqera Tower and add tower yaml for reports by @slsevilla in #92
• Dev store downsample data by @chrisgulvik in #94
• Dev to main by @chrisgulvik in #96

New Contributors

• @slsevilla made their first contribution in #92

Added

• Consistent metrics reported for each read cleaning step (@chrisgulvik)
• Added SeqFu for FastQ format validation (@chrisgulvik)
• Checksum (SHA-512) reporting of intermediate and output files (@chrisgulvik)
• Report full input paths for each sample (@chrisgulvik)
• For assembly depth reporting, added stdev depth metrics; added total paired+single mapped stats (@chrisgulvik)

Changed

• Default uses SeqKit rather than SeqTk for downsampling (@chrisgulvik)
• Output structure and filenames revised (@chrisgulvik)
• For MLST, exclude all MLST databases with a *_ by default (> 1) to ensure the original MLST database version is used for each taxon (e.g., excludes leptospira_2 and leptospira_3) and avoids inconsistent versions used within a run which would occasionally give one sample a leptospira and a different sample leptospira_3 making it impossible to immediately compare between samples. (@chrisgulvik)
• For MLST, store novel FastA when that situation occurs (@chrisgulvik)
• Sample name in outputs and file content no longer contains assembler name (@chrisgulvik)
• Changed RDP output to exclude unneccesary data columns such as "Phylum\nphylum", "Genus\ngenus" (@chrisgulvik)
• Use both R1 and R2 and only Phred30 for estimate bp input for more accurate estimation of genome size (@chrisgulvik)
• Changed default to always on to store stats and FastA of discarded contigs during biopython filtering (@chrisgulvik)
• Output filenames within pipeline_info/ changed to show month by name and include day of the week (@chrisgulvik)

Fixed

• Order of operations in Trimmomatic process now ensures final output reads have minimum sequence length (default: 50 bp) (@chrisgulvik)
• Fixed issue with missing column header names in the .kraken_summary.tsv output files (@chrisgulvik)
• Fixed trailing tab character in Kraken1 and Kraken2 output TSV summaries, which made pandas XLSX conversion fail due to different column numbers in header and data (@chrisgulvik)
• Fixed VERSION reporting RDP bug by removing spaces (@chrisgulvik)

Updated

• Coloring of workflow process now corresponds to tab color in XLSX output summary sheet (@chrisgulvik)
• Docker container version updates (@chrisgulvik)
• Updated description on output files based on new files created as well as some renamed output files (@chrisgulvik)

Deprecated

• Removed gene calling from QUAST output summary (@chrisgulvik)

Full Changelog: v2.3.0...v3.0.0