v1.0.0

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