What's Changed
- initial workflow setup by @anwarMZ in #1
- nextflow version updated by @anwarMZ in #2
- Add krona/samtools/untar modules by @matnguyen in #3
- Miguel dev by @azmigueldario in #9
- Merging taxonomy branch into dev by @anwarMZ in #12
- Nanopore workflow by @matnguyen in #13
- Exposed dragonflye/shovill parameters to modules.config by @matnguyen in #15
- Moved concatenation of nanopore sequencing runs to outside of QC by @matnguyen in #17
- Update assembly QC parameter descriptions by @jimmyliu1326 in #14
- David by @davidtong28 in #20
- Changes to rasusa and confindr by @ASridhar94 in #18
- Updated assembly_qc.nf by @jimmyliu1326 in #21
- Handling null values in assembly QC by @jimmyliu1326 in #22
- Updated conf/eagle_2.config by @davidtong28 in #23
- Fixed issue with Samtools fastq being unable to work on nanopore sequences by @matnguyen in #24
- Added parameter checking for all databases and bugfixes to BUSCO by @matnguyen in #25
- Fixed error related to checkm_db parameter by @jimmyliu1326 in #26
- update main file for multiple worklfow options by @anwarMZ in #42
- #34 create a sub workflow for plasmid prediction by @jimmyliu1326 in #46
- 41 create a nextflow module for crisprcastyper by @jimmyliu1326 in #45
- migrated qc database checks from main to seqqc workflow by @jimmyliu1326 in #50
- 30 create a nextflow module for resfinder by @KijinKims in #53
- #33 create a nextflow module for virsorter2 by @jimmyliu1326 in #52
- Updated Readme file and conf/test.config. Shovill not working by @mayee123 in #56
- #38 sub-workflow for pangenome analysis by @jonathho in #55
- #31 sub-workflow for phage prediction by @jimmyliu1326 in #51
- 32 sub workflow for gene annotation by @anwarMZ in #44
- fixing typos in the gene_annotation by @anwarMZ in #57
- modules for amrprediction in amr_annotation subworkflow by @anwarMZ in #47
- #39 CRISPR Subworkflow by @jimmyliu1326 in #59
- 28 workflow for genome annotation by @anwarMZ in #58
- Cleaned up dev branch by @anwarMZ in #60
- Re-branding nf-seqqc to bacpaq by @anwarMZ in #61
- add customized multiqc config file by @azmigueldario in #62
New Contributors
- @anwarMZ made their first contribution in #1
- @matnguyen made their first contribution in #3
- @azmigueldario made their first contribution in #9
- @jimmyliu1326 made their first contribution in #14
- @davidtong28 made their first contribution in #20
- @ASridhar94 made their first contribution in #18
- @KijinKims made their first contribution in #53
- @mayee123 made their first contribution in #56
- @jonathho made their first contribution in #55
Full Changelog: https://github.com/cidgoh/bacpaq/commits/v1.0.0