v3.0.6

Main change was to fix bug with the "kraken" pipeline where downloading the minikraken database worked the first time, but if you tried running samples a second time, only the first sample would be processed.

Other small changes:

• update to link on installation document (thanks @abissett)
• update to help message and reporting which pipeline is being run
• upload example host index and include as default parameter
• upload MEGARes v3 database bwa index and include as default parameter

v3.0.5

This release includes:

• an update to the docker container, bringing python to v3.9 to work with AmrPlusPlus_SNP
• cleaning up extra docker files

Hotfix - Third time's the charm!

Another hotfix to mistake associated with a process' "tag" vs "label".
Small changes to some other process tags, but otherwise no major updates.

v3.0.3: Merge pull request #22 from Microbial-Ecology-Group/dev

• small fixes to sample ID name handling, particularly an issue when running the "bam_resistome" pipeline.
• added the "align" pipeline to only carryout alignment to a bwa database
• added better tag descriptions
• expanded help menu

v3.0.2

Hotfix changes thanks to @felipemachado85 and @mdhfz89.

Changes:

• Quick fix to naming of "reference" variable to "host"
• Revert to original code for samtools view during host removal module.

v3.0.1

Updates in this version v3.0.1:

• Updates to work with the latest SNP confirmation software.
• Addition of option to specify "--amr_index" and "--host_index" and skip the automatic creation of the bwa index
• Automate download of minikraken_8GB_202003 database when using kraken.
• Fixes to handling unmapped paired reads during host removal. Only keeping paired reads when neither read aligned to the host.
• Fixes to singularity config file.
• Updates to READ.ME