bacpaq - v1.0.1

What's Changed

• Fixed typo for multiqc definition in configuration by @anwarMZ in https://github.com/cidgoh/bacpaq/pull/64
• update github actons by @anwarMZ in https://github.com/cidgoh/bacpaq/pull/70
• Fixed the error related to empty lists passed to reads arrays in bacpaq by @anwarMZ in https://github.com/cidgoh/bacpaq/pull/66
• update github actons by @anwarMZ in https://github.com/cidgoh/bacpaq/pull/71
• Squashed some bugs and added automation to the slack genomics group by @anwarMZ in https://github.com/cidgoh/bacpaq/pull/72

Full Changelog: https://github.com/cidgoh/bacpaq/compare/v1.0.0...v1.0.1

- Nextflow
Published by anwarMZ over 1 year ago

bacpaq - v1.0.0

What's Changed

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

New Contributors

• @anwarMZ made their first contribution in https://github.com/cidgoh/bacpaq/pull/1
• @matnguyen made their first contribution in https://github.com/cidgoh/bacpaq/pull/3
• @azmigueldario made their first contribution in https://github.com/cidgoh/bacpaq/pull/9
• @jimmyliu1326 made their first contribution in https://github.com/cidgoh/bacpaq/pull/14
• @davidtong28 made their first contribution in https://github.com/cidgoh/bacpaq/pull/20
• @ASridhar94 made their first contribution in https://github.com/cidgoh/bacpaq/pull/18
• @KijinKims made their first contribution in https://github.com/cidgoh/bacpaq/pull/53
• @mayee123 made their first contribution in https://github.com/cidgoh/bacpaq/pull/56
• @jonathho made their first contribution in https://github.com/cidgoh/bacpaq/pull/55

Full Changelog: https://github.com/cidgoh/bacpaq/commits/v1.0.0

- Nextflow
Published by anwarMZ over 1 year ago