nf-core/rnaseq v3.2 - Copper Flamingo

[3.2] - 2021-06-18

Enhancements & fixes

• Removed workflow to download data from public databases in favour of using nf-core/fetchngs
• Added a stand-alone Python script bin/fastq_dir_to_samplesheet.py 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 --salmon_quant_libtype parameter to provide the --libType option to salmon quantification
• [#645] - Remove trailing slash from params.igenomes_base
• [#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
--public_data_ids
--skip_sra_fastq_download
	--salmon_quant_libtype

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.