nf-core/rnaseq: nf-core/rnaseq v3.4 - Aluminium Aardvark

[3.4] - 2021-10-05 Enhancements &amp; fixes Software version(s) will now be reported for every module imported during a given pipeline execution Added <code>python3</code> shebang to appropriate scripts in <code>bin/</code> 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 <code>--bbsplit_fasta_list</code> <code>--bbsplit_index</code> <code>--save_bbsplit_reads</code> <code>--skip_bbsplit</code> <strong>NB:</strong> Parameter has been <strong>updated</strong> if both old and new parameter information is present. <strong>NB:</strong> Parameter has been <strong>added</strong> if just the new parameter information is present. <strong>NB:</strong> Parameter has been <strong>removed</strong> 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 <code>bbmap</code> 38.93 <code>hisat2</code> 2.2.0 2.2.1 <code>picard</code> 2.23.9 2.25.7 <code>salmon</code> 1.4.0 1.5.2 <code>samtools</code> 1.12 1.13 <code>sortmerna</code> 4.2.0 4.3.4 <code>trim-galore</code> 0.6.6 0.6.7 <strong>NB:</strong> Dependency has been <strong>updated</strong> if both old and new version information is present. <strong>NB:</strong> Dependency has been <strong>added</strong> if just the new version information is present. <strong>NB:</strong> Dependency has been <strong>removed</strong> if version information isn't present.