nf-core/rnaseq: nf-core/rnaseq v3.2 - Copper Flamingo

[3.2] - 2021-06-18 Enhancements &amp; fixes Removed workflow to download data from public databases in favour of using nf-core/fetchngs Added a stand-alone Python script <code>bin/fastq_dir_to_samplesheet.py</code> to auto-create samplesheet from a directory of FastQ files Added docs about overwriting default container definitions to use latest versions e.g. Pangolin [#637] - Add <code>--salmon_quant_libtype</code> parameter to provide the <code>--libType</code> option to salmon quantification [#645] - Remove trailing slash from <code>params.igenomes_base</code> [#649] - DESeq2 fails with only one sample [#652] - Results files have incorrect file names [nf-core/viralrecon#201] - Conditional include are not expected to work Parameters Old parameter New parameter <code>--public_data_ids</code> <code>--skip_sra_fastq_download</code> <code>--salmon_quant_libtype</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.