v1.4.3

Adopt latest version of the NCBI SRA-Human-Scrubber tool that addresses previous issue regarding the inadvertent impact on the quality of SC2 genome assemblies generated with the Titan workflows for genomic characterization in v1.4.1

Updates to the ncbi_scrub_pe and ncbi_scrub_se tasks:

• NCBI Scrubber docker tag updated to latest release: ncbi/sra-human-scrubber:1.0.2021-05-05
• -n flag invoked with scrubber.sh command to ensure that human reads are replaced with IUPAC N rather than fully removed from read files
  • Additional outputs to capture the number of human sports removed

Modified workflows:

• ncbi_scrub_pe and ncbi_scrub_se modified to use updated task and output number of human spots removed
• Titan_Illumina_PE, Titan_ONT & Titan_ClearLabs modified to incorporate host-removal as first step; extra kraken run added after dehosting to check impact on the percentage of human & SC2 reads
  • New outputs for Titan_ClearLabs & Titan_ONT: dehosted_reads, fastqc_clean, kraken_human_deshoted, kraken_sc2_dehosted, kraken_report_deshoted
  • New outputs for Titan_Illumina_PE: dehosted_read1, dehosted_read2, kraken_human_deshoted, kraken_sc2_dehosted, kraken_report_deshoted
  • Note: the updated NCBI scrubber tasks were not incorporated into the Titan_Illumina_SE workflow since the smaller size read data are not compatible with host-removal with this tool

Other repo changes:

• Default pangolin tag for Titan workflows for genomic characterization set to staphb/pangolin:2.4.2-pangolearn-2021-05-19
• Updated default minlength for the trimmomatic task to 75
  • No workflows impacted as explicit minlengths are provided in the workflows that utilize this task