v26.5.28

What's Changed

• Add PyPI badge to README by @Copilot in #143
• Fix sequana_taxonomy unclassified option by @cokelaer in #144
• Fix shells.yml by @cokelaer in #145
• Implement unclassified reads extraction in sequana_taxonomy by @cokelaer in #146

Full Changelog: v26.4.16...v26.5.28

v26.4.16

What's Changed

• add SE/PE for fastp by @cokelaer in #142

Full Changelog: v26.4.7...v26.4.16

v26.4.7

What's Changed

• add v2 for bwa by @cokelaer in #137
• Fix bz2_to_gz command and CI issues by @cokelaer in #138
• Fix apptainer workflow: missing package install and invalid expression function by @Copilot in #139
• fixing 3 shells by @cokelaer in #140
• Fix snpeff shell: configure genome and place GenBank file in expected… by @cokelaer in #141

Full Changelog: v26.4.1...v26.4.7

v26.4.1

What's Changed

• add shells modules (bowtie2, bwa, minimap2, feature_counts, multiqc, … by @cokelaer in #114
• Enhance shell modules, tests, and CI configurations by @cokelaer in #136

Full Changelog: v25.11.16...v26.4.1

v26.3.24

What's Changed

• Fix CI for PyPI deployment by @cokelaer in #122
• Add test.py file by @cokelaer in #123
• Clean up unused tests and fix related issues by @cokelaer in #127
• Add missing files and Polypolish test by @cokelaer in #128
• Add shell modules and tests for add_read_group, bowtie1, busco, deeptools, digital_normalisation, freebayes_parallel, samtools_depth, sequana_taxonomy, star, unicycler by @Copilot in #129
• Fix Makefile and add missing index file for Bowtie1 and others by @cokelaer in #130
• Fix infernal wrappers: correct test paths, add README, wire extra param by @Copilot in #132
• Fix tests and update README and Makefile by @cokelaer in #131
• add sambamba markdup by @cokelaer in #133
• Update CI metadata and remove metaka by @cokelaer in #135

New Contributors

• @Copilot made their first contribution in #125

Full Changelog: v26.3.21...v26.3.24

v26.3.21

What's Changed

• Fix Poetry build and PyPI CI by @cokelaer in #120
• Add MACS3 and mark duplicates functionality by @cokelaer in #121

Full Changelog: v26.3.20...v26.3.21

v26.3.20

What's Changed

• add shells modules (bowtie2, bwa, minimap2, feature_counts, multiqc, … by @cokelaer in #114
• add snippets modules by @cokelaer in #118

Full Changelog: v25.11.16...v26.3.20

v24.8.29

What's Changed

• Update unicycler wrapper by @cokelaer in #111

Full Changelog: v24.2.6...v24.8.29

v24.2.6

What's Changed

• Adding infernal from main sequana-wrappers repo and minor blast makedb fix by @khourhin in #109
• add new wrapper for freebayes-parallel by @cokelaer in #110
• Fix typo in sequana_coverage to use annotation file

Full Changelog: v24.1.14...v24.2.6

v24.1.14

What's Changed

• Fix missing window_size in sequana coverage wrapper by @cokelaer in #108

Full Changelog: v24.1.8...v24.1.14