[3.4] - 2021-10-05 Enhancements & fixes Software version(s) will now be reported for every module imported during a given pipeline execution Added python3 shebang to appropriate scripts in bin/ directory [#407] - Filter mouse reads from PDX samples [#570] - Update SortMeRNA to use SilvaDB 138 (for commercial use) [#690] - Error with post-trimmed read 2 sample names from FastQC in MultiQC [#693] - Cutadapt version missing from MultiQC report [#697] - pipeline_report.{txt,html} missing from pipeline_info directory [#705] - Sample sheet error check false positive Parameters Old parameter New parameter --bbsplit_fasta_list --bbsplit_index --save_bbsplit_reads --skip_bbsplit NB: Parameter has been updated if both old and new parameter information is present. NB: Parameter has been added if just the new parameter information is present. NB: Parameter has been removed if parameter information isn't present. Software dependencies Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference. Dependency Old version New version bbmap 38.93 hisat2 2.2.0 2.2.1 picard 2.23.9 2.25.7 salmon 1.4.0 1.5.2 samtools 1.12 1.13 sortmerna 4.2.0 4.3.4 trim-galore 0.6.6 0.6.7 NB: Dependency has been updated if both old and new version information is present. NB: Dependency has been added if just the new version information is present. NB: Dependency has been removed if version information isn't present.