BleekerLab/small-rna-seq-pipeline: Release 0.4.0

New functionalities added:

• Now outputs a concatenated Shortstack file called "concatenated_shortstacks.tsv" that contains all predicted sRNA loci from all samples. Small RNA loci corresponding to a MIR gene hairpin will have the hairpin sequence added. Finally, a unique cluster id (column "cluster_unique_id") is added so that all individual sRNA loci from every sample will have a unique identifier. That can be useful when several sRNA loci correspond have a common MIR gene homolog in miRBase for instance.

• Uses a "samples.tsv" file to list the sample names, their fastq file location and the genomic reference to use.

• Calculate the minimal folding energy for all predicted hairpins using Vienna RNA RNAfold program. This information can be used to fold the stem-loop structure of hairpins (using the RNAplot program from Vienna RNA package).