This release caps cutadapt under 4.0 and fix generation of STAR/RSEM references.

• keep cutadapt strictly under 4.0 until #72 is resolved
• fix STAR/RSEM reference
• handle FASTA file ending with .fna when preparing STAR/RSEM reference

This release update MultiQC and Pandas.

• update MultiQC to 1.12
• remove version cap for Pandas by fixing the writing in binary mode
• use Python 3.10 for the CI
• respect PAIRED in SRA runinfo metadata

This patch release addresses a couple of minor issues, update MultiQC and include a JSON report for cutadapt.

• update MultiQC to 2.11
• generate a cutadapt JSON report alongside trimmed reads and add it to MultiQC search directories
• add a new --ignore-priority option to SubmitExperimentsFromFileToGemma and SubmitExperimentsFromGoogleSpreadsheetToGemma
• fix output when --ignore-mate=forward is passed to TrimSample task
• raise an exception for empty SRA record instead of creating an empty file

This patch release introduces a safer way of passing password to the Gemma CLI and fix issue of long-running align sample tasks.

This patch release introduces a new CI based on GitHub Actions and migrate Gemma tasks to use the new Gemma CLI.