Age | Commit message (Collapse) | Author | |
---|---|---|---|
2020-09-04 | added in the sra script an option to include only a subset of ids | AndreaGuarracino | |
2020-09-04 | sra script updated for managing more locations | AndreaGuarracino | |
2020-09-04 | synchronized the create_sra_metadata.py script with the latest updates | AndreaGuarracino | |
2020-08-29 | fixed few countries ontology terms; added a new species | AndreaGuarracino | |
2020-08-28 | added script to remove entries on Arvados | AndreaGuarracino | |
2020-08-28 | local QC is optional | AndreaGuarracino | |
2020-08-28 | added control (locally and in the validation) that sample_id has to be the ↵ | AndreaGuarracino | |
same in the metadata and in the FASTA header #103 | |||
2020-08-28 | qc_fasta returns also the seq_type; verified that only one FASTA is sent at ↵ | AndreaGuarracino | |
a time; code cleaning | |||
2020-08-28 | fixed local QC, modifying the regex for FASTA/FASTQ to be more general | AndreaGuarracino | |
2020-08-27 | updated dependency from clustalw to minimap2; the genbank script no longer ↵ | AndreaGuarracino | |
creates YAML/FASTA pairs for too short sequences | |||
2020-08-26 | Increase RAM for odgi-build-from-spoa-gfa | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-08-26 | updated parameter name | AndreaGuarracino | |
2020-08-26 | added option in the genbank script to ignore (already validated) IDs; code ↵ | AndreaGuarracino | |
cleaning; typos | |||
2020-08-26 | typos in the code; little code refactoring | AndreaGuarracino | |
2020-08-26 | Docs | Pjotr Prins | |
2020-08-26 | Fix underscores | Pjotr Prins | |
2020-08-25 | Increase RAM requirement for sort_fasta_by_quality_and_len | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-08-25 | Using Arvados | Pjotr Prins | |
2020-08-25 | the YAML/FASTA pair is not created for samples where at least one mandatory ↵ | AndreaGuarracino | |
field is missing | |||
2020-08-24 | fixed protocol for the dictionary entries that caused validation problems | AndreaGuarracino | |
2020-08-24 | Fix dependency conflict with PyShExC | Peter Amstutz | |
2020-08-24 | Adding meta keywords to HTML | Pjotr Prins | |
2020-08-24 | genbank script documented in blog | Pjotr Prins | |
2020-08-24 | reverted the relaxation on the location attribute | AndreaGuarracino | |
2020-08-24 | Merge pull request #102 from AndreaGuarracino/patch-4 | Pjotr Prins | |
a lot of new ontology terms, genbank/sra scripts updated to be more general | |||
2020-08-24 | Genbank upload | Pjotr Prins | |
2020-08-24 | Add note on most fields being optional | Pjotr Prins | |
2020-08-24 | Images | Pjotr Prins | |
2020-08-23 | More info | Pjotr Prins | |
2020-08-23 | Textual changes | Pjotr Prins | |
2020-08-23 | genbank/sra scripts update to be more generic with the specimen sources | AndreaGuarracino | |
2020-08-23 | added new countries and speciesman sources: fixed few country entries | AndreaGuarracino | |
2020-08-22 | genbank/sra scripts updated to read the dictionaries in a more general way | AndreaGuarracino | |
2020-08-22 | lots of new dictionary terms | AndreaGuarracino | |
2020-08-22 | Generated | Pjotr Prins | |
2020-08-22 | Relaxing the location attribute | Pjotr Prins | |
2020-08-22 | FASTQ in capitals | Pjotr Prins | |
2020-08-22 | More on contacting | Pjotr Prins | |
2020-08-22 | Repositioning content | Pjotr Prins | |
2020-08-22 | Reorganize footer | Pjotr Prins | |
2020-08-22 | Reworded blurb | Pjotr Prins | |
2020-08-22 | Small text fixes | Pjotr Prins | |
2020-08-22 | guix-deploy script | Pjotr Prins | |
2020-08-20 | Update links to reflect latest workflow | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-08-19 | Fix output parameters | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-08-19 | Scaling pangenome generation | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-08-19 | Consolidate steps to scale graph generation workflow | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-08-19 | Merge pull request #101 from AndreaGuarracino/patch-3 | Peter Amstutz | |
used builtin hashlib md5 for the deduplication step | |||
2020-08-19 | used builtin hashlib md5 for the deduplication step | AndreaGuarracino | |
2020-08-19 | Merge pull request #100 from AndreaGuarracino/patch-3 | Peter Amstutz | |
integrated the deduplication step in the sorting by quality and length script |