CHANGELOG.md

nf-core/kmermaid: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v0.1.0dev - [date]

Initial release of nf-core/kmermaid, created with the nf-core template.

Added

• Add option to use Dayhoff encoding for sourmash.
• Add bam2fasta process to kmermaid pipeline and flags involved.
• Add extract_coding and peptide_bloom_filter process and flags involved.
• Add track_abundance feature to keep track of hashed kmer frequency.
• Add social preview image
• Add fastp process for trimming reads
• Add option to use compressed .tgz file containing output from 10X Genomics' cellranger count outputs, including possorted_genome_bam.bam and barcodes.tsv files
• Add samtools_fastq_unaligned and samtools_fastq_aligned process for converting bam to per cell barcode fastq
• Add version printing for sencha, bam2fasta, and sourmash in Dockerfile, update versions in environment.yml
• For processes translate, sourmash compute add cpus=1 as they are only serial (#107)
• Add sourmash sig merge for aligned/unaligned signatures from bam files, and add --skip_sig_merge option to turn it off
• Add --protein_fastas option for creating sketches of already-translated protein sequences
• Add --skip_compare option to skip sourmash_compare_sketches process
• Add merging of aligned/unaligned parts of single-cell data (#117)
• Add renamed package dependency orpheum (used to be known as sencha)

Fixed

Resources

• Increase CPUs in high_memory_long profile from 1 to 10

Naming

• Rename splitkmer to split_kmer

Per-cell fastqs and bams

• Remove one_signature_per_record flag and add bam2fasta count_umis_percell and make_fastqs_percell instead of bam2fasta sharding method
• Use ripgrep instead of bam2fasta to make per-cell fastq, which will hopefully make resuming long-running pipelines on bams much faster
• Make sure samtools_fastq_aligned outputs ALL aligned reads, regardless of mapping quality or primary alignment status

Sourmash

• add --skip_compute option to skip sourmash_compute_sketch_*
• Used .combine() instead of each to do cartesian product of all possible molecules, ksizes, and sketch values
• Do sourmash compute on all input ksizes, and all peptide molecule types, at once to save disk reading/writing efforts

Translate

• Updated sencha=1.0.3 to fix the bug in memory errors possibly with the numpy array on unique filenames (PR #96 on orpheum)
• Add option to write non-coding nucleotide sequences fasta files while doing sencha translate
• Don't save translate csvs and jsons by default, add separate --save_translate_json and --save_translate_csv
• Updated sencha translate default parameters to be --ksize 8 --jaccard-threshold 0.05 because those were the most successful
• Update renaming of khtools commands to sencha

MultiQC

• Fix the use of skip_multiqc flag condition with if and not when

Dependencies

Deprecated

• Removed ability to specify multiple --scaled or --num-hashes values to enable merging of signatures