Changes
- Fixed a bug introduced by a change in AssemblyUtil that moved a file produced by AU.
Changes
- Removed datatype of "KBaseGenomeAnnotations.Assembly" in the hybridSPAdes narrative input ui spec because this datatype is not supported by SPAdes itself.
- dropped the minimum memory threshold in /lib/kb_SPAdes/utils/spades_utils.py MIN_MEMORY_GB from 5 to 4 to fit in Github Actions test node
Changes
- updated SPAdes to 3.15.3
- dropped kb_SPAdesImpl.py MIN_MEMORY_GB from 5 to 4 to fit in Github Actions test node
- changed default output object name to <method_name>.Assembly
Changes
- updated SPAdes to 3.15.2
- added github actions tests
- made unit test data upload via ReadsUtil.upload_reads()
- fixed broken unit tests
- completed port from python 2 to 3
Changes
- removed HTML from input params to hybridSPAdes
Changes
- matched the pacbio* strings from within the main code to the values in the ui dropdown
Changes
- update docs
Changes
- updated to 3.13 and added hybrid spades feature
Changes
- added citations in PLOS format
Changes
- updated to SPAdes 3.12.0
Changes
- added advanced parameters to set list of Kmer sizes and option to skip read error correction
Changes
- changed contact from email to url
Changes
- updated version of SPAdes to 3.11.1
Changes
- updated metaSPAdes() min_contig_length parameter to required and changed default values to min:300bp default: 2Kbp
Changes
- Added min_contig_length parameter for metaSPAdes
- Limited MetaSPAdes narrative UI to accept only one reads input
- Limit SPAdes and MetaSPAdes memory usage to 100GB and 500GB respectively.
- Removed requirement for 'single_genome' flag not set for metagenomic assembly
- Added travis CI