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pathogenseq v1.0.4
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@xiaoli-dong xiaoli-dong released this 30 Jan 15:53
· 14 commits to main since this release
v1.0.4
b2bc2e0

Added de-host module using hostile. By default, the de-hosting function is enabled. You can disable or enable function using the following command line options.

  • " --skip_illumina_dehost true"
  • "--skip_nanopore_dehost true"

Added minimum data in base pair requirement command line options for proceeding to the assembly step:

  • "--min_tbp_for_assembly_illumina", the default value is 1000000 bp
  • "--min_tbp_for_assembly_nanopore", default value is 1000000 bp

Added pathogen specific tools and you can disable or enable the tools using command line options: "

  • emmtyper for streptococcus pyogenes emm typing. you can disable or enable the function through command line options "--skip_emmtyper false". By default, the function is disabled.
  • tb-profiler for Mycobacterium tuberculosis whole genome analysis. you can disable or enable the function through command line options "--skip_tbprofiler false". By default, the function is disabled.
  • pneumocat for Streptococcus pneumoniae capsular typing. you can disable or enable the function through command line options "--skip_peuumocat false". By default, the function is disabled.
  • GBS-SBG tools for Group B Streptococcus serotyping. you can disable or enable the function through command line options "--skip_gbssbg false". By default, the function is disabled.

When there are not enough input data, some of the tools (dnaapler, shovill, pneumocat, tbprofiler ) included in the pipeline will produce error instead of exit nicely. this will cause the whole pipeline aborting. I change the error handling strategy to ignore, with this strategy, when the tools failed, it will issue warning message and proceed to the next sample or next step of the pipeline instead of the whole pipeline failing.

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