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aladdin-shotgun: Changelog

v0.0.6

Added

  • Added antimicrobial resistance genes with AMRplusplus.
  • An experimental function to highlight the abundance of taxa of interest. The first experimental organism list is wastewater related organisms obtained from LA County Sanitation District.

v0.0.5

Changed

  • Sourmash output now uses sequence IDs (assembly accession numbers) as keys. Pipeline now generates a Qiime2 feature table with these keys, in addition to the table with collapsed taxonomy.
  • MultiQC report has a title that matches the run name. User can use -name to change the report title.

v0.0.4

Added

  • Visualizations for taxonomy profiling results in the report.
  • Diversity analysis using Qiime2. Including exporting taxonomy results to Qiime2, merge/filter samples, alpha rarefaction, alpha/beta diversity.
  • Diveristy visualizations including heatmaps, alpha rarefaction curve, alpha/beta diversity plots.
  • Filtering of samples or taxa based on low read count, minimum reads per taxa, minimum sample per taxa.
  • New profiler: sourmash.
  • Zymo's sourmash database, which contains host sequences. Added support scripts to separate host reads from rest, and correspoding MultiQC visualizations.
  • Optional khmer trim-low-abund.py for sourmash.
  • Compare with a reference dataset using Qiime2.
  • A process to generate an output manifest JSON file, part of compatibility requirements for Aladdin.

Changed

  • Metaphan 3 changed to metaphlan 4
  • User must choose one profiler-database combination, instead of running multiple profilers. Temporarily disabled profilers except sourmash and metaphlan4.
  • Changed the format of sample sheet, aka. design CSV file and the code that sanity checks this file.
  • Temporarily disabled support for Nanapore data.
  • Tie read length filtering in preprocessing to kmer size, when sourmash is selected.
  • Ignore samples that failed read QC or profiling. Let pipeline finish successfully regardless of a few bad samples. Add warnings for failed samples to report.
  • Hide most parameters from Aladdin users.
  • Use Aladdin report template.
  • Eliminated 'perform_shortread_qc' and 'perform_shortread_complexityfilter' paramters and merged them into others.

Fixed

  • Sample name cleaning in report. Now one sample occupy one row in the general stats table.
  • FastQC results not correctly fed to MultiQC for single-end data.

Removed

  • nf-core related files and code that are not required any more.

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