bh20-seq-resource/workflows/pangenome-generate, branch new_assembly_method_field Tool to upload SARS-CoV-2 sequences to BH20 Arvados instance and orchestrate analysis http://git.systemreboot.net/bh20-seq-resource/atom?h=new_assembly_method_field 2020-09-26T10:12:17+00:00 script for processing the metadata of the ESR samples; moved delete_entries_on_arvados script in scripts directory 2020-09-26T10:12:17+00:00 AndreaGuarracino 2020-09-26T10:12:17+00:00 urn:sha1:7c12e4976337a063301be260cb3954bf4303f5e0 added script to remove entries on Arvados 2020-08-28T15:36:30+00:00 AndreaGuarracino 2020-08-28T15:36:30+00:00 urn:sha1:ef4e55ce81448088b1e730a12d6772ebc01ce8af Increase RAM for odgi-build-from-spoa-gfa 2020-08-26T21:36:12+00:00 Peter Amstutz 2020-08-26T21:36:12+00:00 urn:sha1:b69b8560132786e16ea6a997d65fd8c43381cc03 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Increase RAM requirement for sort_fasta_by_quality_and_len 2020-08-25T18:23:57+00:00 Peter Amstutz 2020-08-25T18:23:57+00:00 urn:sha1:13051e1ad29be14e06d96565cd5f0d12621a63aa Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Fix output parameters 2020-08-19T20:31:38+00:00 Peter Amstutz 2020-08-19T20:31:26+00:00 urn:sha1:25bab899cbe8871cbb9530fc768a1cd7ab4daba1 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Scaling pangenome generation 2020-08-19T20:31:38+00:00 Peter Amstutz 2020-08-19T19:15:57+00:00 urn:sha1:d1e8809a15ae74d0b847abb80f9f63f53078e1d6 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Consolidate steps to scale graph generation workflow 2020-08-19T20:31:38+00:00 Peter Amstutz 2020-08-19T19:19:07+00:00 urn:sha1:b3d2ccf951903ac0b7d717357fb1cccca26fbd15 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> used builtin hashlib md5 for the deduplication step 2020-08-19T20:29:33+00:00 AndreaGuarracino 2020-08-19T20:29:33+00:00 urn:sha1:4fe8876d6ff17479a36ebcce564aa6983e15c490 integrated the deduplication step in the sorting by quality and length script 2020-08-19T15:59:39+00:00 AndreaGuarracino 2020-08-19T15:59:39+00:00 urn:sha1:0cee8cc13b869ef389c941f662c3cef2409e1e61 added workflow to sort a multifasta by quality and length, and added the overall new pangenome generation workflow with SPOA 2020-07-27T15:27:07+00:00 AndreaGuarracino 2020-07-27T15:27:07+00:00 urn:sha1:618f956eb03c6a6ad1cc16efc931f55b0dce83e1