Releases · cidgoh/bacpaq

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