pathogenseq - pathogenseq v1.1.4

fixed a bug that pipeline will fail when the inputs to dehosting were empty for nanopore data

Full Changelog: https://github.com/xiaoli-dong/pathogenseq/compare/v1.1.3...v1.1.4

- Nextflow
Published by xiaoli-dong about 1 year ago

pathogenseq - pathogenseq

To reflect the armfinderplus database schema change, the following software has been updated:

• bakta (1.9.2 -> 1.9.4)
• ncbi-amrfinderplus ( 3.11.18 -> 3.12.8)

Tbprofiler has been changed from 5.0.1 to 6.2.1

- Nextflow
Published by xiaoli-dong over 1 year ago

pathogenseq - pathogenseq v1.1.0

• Fixed a bug associated with Polypolish and polca short read polish process. This was caused by the mis-association of the input reads and contigs during the mapping. It means the reads mapped to the contigs from the other samples.
• Fixed a bug associated with the long reads assembly. The pipeline would crash when there were no short reads available.
• Updated the versions of the following tools:
  • samtools (1.16.1 -> 1.19.2)
  • fastqc (0.11.9->0.12.1)
  • mlst (2.19.0 -> 2.23.0)
  • bakta (1.6.1->1.9.2)
  • nanoplot(1.41.0->1.41.6)

- Nextflow
Published by xiaoli-dong almost 2 years ago

pathogenseq - pathogenseq

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.

• " --skipilluminadehost true"
• "--skipnanoporedehost true"

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

• "--mintbpforassemblyillumina", the default value is 1000000 bp
• "--mintbpforassemblynanopore", 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.

- Nextflow
Published by xiaoli-dong about 2 years ago

pathogenseq - pathogenseq v1.0.3

• Assembly stats were generated using "seqkit stats" and change the program to assembly-stats
• In the reads stats table, changed the first column to sample id instead of using sequence file name.
• Added mobtyper produced contigreport.txt files, which describes the assignment of the contig to chromosome or a particular plasmid grouping.
  

- Nextflow
Published by xiaoli-dong about 2 years ago

pathogenseq - pathogenseq v1.0.2

• Reformatted the output sample id: get rid of "_T" suffix
• Added shovill assembler, which can do down sampling

- Nextflow
Published by xiaoli-dong over 2 years ago

pathogenseq - pathogenseq v1.0.1

1. Added assembled contig depth information by mapping qc reads to contigs
2. Changed the samplesheet from seven columns to five columns, removed "genome_size" and "fast5" columns
3. Changed basecallermode value from "fast|hac|sup" to medaka allowed model value, such as "r1041e82400bpssup_v4.2.0"
4. Upadted nextflow_schema files to make the pipeline command line options are more readable

- Nextflow
Published by xiaoli-dong over 2 years ago

pathogenseq - pathogenseq v1.0.0

Full Changelog: https://github.com/xiaoli-dong/pathogenseq/commits/v1.0.0

- Nextflow
Published by xiaoli-dong over 2 years ago