Skip to content

Latest commit

 

History

History
70 lines (47 loc) · 3.42 KB

CHANGELOG.md

File metadata and controls

70 lines (47 loc) · 3.42 KB
Raw

nf-core/kmermaid: Changelog

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

v1.0.0dev

The content below is the unaltered changelog of the unreleased 2020 version of the pipeline.

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.