v1.1.2

What's Changed

• Update dev to latest main by @hoelzer in #116
• add pacbio specific minimap2 parameter and input option by @hoelzer in #117
• Dev by @hoelzer in #118

Full Changelog: v1.1.1...v1.1.2

v1.1.1

What's Changed

• Try to resolve intermittant conda-related CI failures by @matthuska in #112
• Change check_own process to not include input files in output by @matthuska in #113

Full Changelog: v1.1.0...v1.1.1

v1.1.0

What's Changed

• Summary file for number and proportion of mapped and unmapped reads by @ayoraind in #106
• Add bwa by @MarieLataretu in #103
• Increase RAM by @hoelzer in #101
• fix bbduk which has no bam channel for the new summary script by @hoelzer in #108
• Dev by @hoelzer in #111

New Contributors

• @ayoraind made their first contribution in #106

Full Changelog: v1.0.3...v1.1.0

v1.0.3

What's Changed

• Set default branch to 'main' instead of the Nextflow default 'master' by @matthuska in #92
• Remove 'conda clean' from GitHub action to avoid random crashes by @matthuska in #96
• Bump github action versions for node 16 -> 20 change by @matthuska in #94
• Add T2T homo sapiens genome as additional auto-download option by @hoelzer in #99
• Dev by @hoelzer in #100

Full Changelog: v1.0.2...v1.0.3

Version v1.0.2

What's Changed

• Add --skip_qc to allow skipping fastqc/nanoplot/multiqc by @matthuska in #90

Full Changelog: v1.0.1...v1.0.2

v1.0.1

What's Changed

• add sc2 autodownload by @hoelzer in #87

Full Changelog: v1.0.0...v1.0.1

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

v1.0.0-beta.2

What's Changed

• Add SARS-CoV-2 as an easy-to-use species by @matthuska in #63
• added proxy information forwarding for Singularity usage (can cause problems on HPCs)

New Contributors

• @matthuska made their first contribution in #63

Full Changelog: v1.0.0-beta.1...v1.0.0-beta.2

v1.0.0-beta.1

What's Changed

• changed minimap2 container by @MarieLataretu in #61

Full Changelog: v1.0.0-beta...v1.0.0-beta.1

v1.0.0-beta

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

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

Usage changes

• input parameter usage:
  • before: --[nano|illumina|illumina_single_end|fasta]
  • now: --input_type [nano|illumina|illumina_single_end|fasta] --input *.fastq