v1.0.0

What's Changed

• Marie lataretu/issue23 by @MarieLataretu in #39
• reference index file incomplete by @MarieLataretu in #41
• Marie lataretu/issue42 by @MarieLataretu in #43
• problem when input files end with clean by @MarieLataretu in #48
• add --split-prefix to minimap2 by @MarieLataretu in #49
• Marie lataretu/issue47 by @MarieLataretu in #50
• Updates for cloud run by @hoelzer in #51
• check for newlines when concat fastas by @MarieLataretu in #53
• Feature clean work dir by @MarieLataretu in #59
• Dev by @MarieLataretu in #54
• Dev by @MarieLataretu in #61
• Add SARS-CoV-2 as an easy to use species by @matthuska in #63
• Fixes a few issues in the ML/issue55 branch by @matthuska in #64
• remove custom log file by @MarieLataretu in #65
• Avoid zcat'ing *.gz when output file is also a .gz file. by @matthuska in #66
• Add bed_samtools container by @matthuska in #69
• Reorganize the results directory by @matthuska in #67
• Marie lataretu/issue55 by @MarieLataretu in #70
• Fix/update-repo-home by @MarieLataretu in #71
• Fix/results-orga-keep by @MarieLataretu in #72
• GitHub Action: Bump setup-miniconda to v3, to support libmamba solver for conda by @matthuska in #73
• Fix/reorganize results by @MarieLataretu in #75
• Fix zcat problems on mac by @matthuska in #77
• Run dryrun action on PR against main or dev, and pushes directly to main by @matthuska in #78
• create an uncompressed index instead of a compressed one by @MarieLataretu in #79
• Dev by @MarieLataretu in #81

New Contributors

• @matthuska made their first contribution in #63

Full Changelog: v0.2.0...v1.0.0