I need to build the following pipeline:
- Upload an SRA file from a remote FTP server (with anonymous access)
- Convert SRA to FASTQ file
- Grooming the FASTQ data
- Upload reference dataset from another remote FTP server
- Map data from steps 3 and 4 with BWA
- Create BAM file from SAM tool
Is it possible to create such a pipeline without using Galaxy UI? Can I make it using only BioBlend? If not, can galaxy API help to create it?