seq2science

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and RNA-seq workflows.

• a check to see if the downloaded fastq from ENA is not empty. Related to a recent internal error (guess) at the side of ENA sending empty fastq files
• a custom message when a rule fails, that redirect to docs

• sample layout lookup is split up in 100's, to avoid a jsondecodeerror which results from very long lists of samples
• the multiqc samples & config tables are generated in a script with its own environment to make base env smaller
• keep_mates for macs2 turned into a script with ts own environment ot make the base env smaller
• seq2science cache now respects the xdg cache
• moved genome downloading rules into scripts instead of run directives, should result in user-friendlier errors

• Fixed scRNA trimming issue
• Added fastq_pair
• Updated schemas
• Added kallistobus examples