Emilio Palumbo

icon company Centre for Genomic Regulation icon location Barcelona

Results 18 issues of Emilio Palumbo

Expose tool options to Nextflow config file

e.g. STAR

Add MultiQC step

http://multiqc.info/

Add pseudo-alignment based quantification tools

- Kallisto - Salmon

Use maps instead of sets for storing samples metadata

Use publishDir to store pipeline results

Allow pipeline to run with no annotation reference file

Use workflows instead of profiles for different pipelines

Redefine processing from input BAM files

In the current implementation input BAM files are merged to the alignment files produced by the pipeline `mapping` step and then used for downstream processing. This approach can pose problems...