Changed
- Several changes have been made to support more types of sequence data (see below).
These changes involve backwards-incompatible changes to syntax. Sequence data types are now:
- fastq-ill-pe - paired-end Illuminq FASTQ data (previously called fastq)
- fastq-ill-se - single-end Illumina FASTQ data
- fastq-ont - Oxford Nanopore FASTQ data
- fasta-asm - FASTA assembly, may be multi-contig
- fasta-cns - single-contig consensus FASTA sequence (previously called fasta)
- The `seq add` command has been updated to support more types of sequence data.
The syntax for uploading single-contig consensus sequences is now `austrakka seq add fasta-cns seqs.fasta`.
The syntax for uploading other types of sequence data is now `austrakka seq add <seqtype> files.csv`.
- The `seq sync get` and `seq get` commands have been updated to support more types of sequence data.
It is now possible to sync multiple types of sequence data from the same group or project to the same output directory.
Sequences will now be downloaded to a subdirectory specific to the sequence type, i.e. <seq_id>/<seqtype>/<file> .
Each sequence type will have a separate state and manifest file.
In the case of fasta-cns data, the aggregated sequence file, previously named all.fasta, is now named consensus.fasta .
- It is now possible to list sequences by sample with the `seq list` command, using a `-s` parameter.
- The admin `seq purge` command now requires a `-t` parameter to specify the sequence type.