index
:
bh20-seq-resource
analysis-refactor
fasta-subset-from-query
generate-cwl
master
new_assembly_method_field
pangenome_workflow_abpoa
upload-download-status
uuid-for-resource
yamlfa2ttl
Tool to upload SARS-CoV-2 sequences to BH20 Arvados instance and orchestrate analysis
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Author
2021-03-17
Use default output of pipeline
generate-cwl
Arun Isaac
2021-03-17
Do not specify outputs to be of File type.
Arun Isaac
2021-03-17
Do not specify inputs to be of File type.
Arun Isaac
2021-03-07
Rewrite fastq2fasta.scm using new ccwl API
Arun Isaac
2021-03-07
Implement bowtie, bwa-mem variant calling in ccwl
Arun Isaac
2021-02-25
Rewrite fastq2fasta workflow using clitool-step
Arun Isaac
2021-02-25
Move generate-cwl to its own repository
Arun Isaac
2021-02-21
Implement fastq2fasta workflows in scheme
Arun Isaac
2021-02-21
Add CWL generator for Workflow workflows
Arun Isaac
2021-02-21
Add CWL generator for CommandLineTool workflows
Arun Isaac
2021-02-21
Add a scm->yaml generator
Arun Isaac
2021-01-28
Jetson test sequence
HEAD
master
Pjotr Prins
2021-01-28
Restored tools submodule
Pjotr Prins
2021-01-28
Moving tools out of submodules (sorry!)
Pjotr Prins
2021-01-28
Adding support for Auspice
Pjotr Prins
2021-01-26
Merge pull request #124 from urbanslug/master
Pjotr Prins
Add phylogeny workflow
2021-01-26
Add phylogeny workflow
Njagi Mwaniki
Signed-off-by: Njagi Mwaniki <njagi@urbanslug.com>
2021-01-08
GenBank: Fix normalization and depth differences with original records
Pjotr Prins
2021-01-08
Set JSON indentation
Pjotr Prins
2021-01-08
Get correct GenBank ID with version, see #122
Pjotr Prins
2021-01-08
FASTA file should not have leading space
Pjotr Prins
2021-01-07
fixed comments in the example yaml files
AndreaGuarracino
2021-01-07
Merge pull request #121 from BonfaceKilz/chore/add-extra-tab-for-all-feeds
Pjotr Prins
Chore/add extra tab for all feeds
2021-01-07
Allow for xml and xml.gz files
Pjotr Prins
2021-01-06
cleaned utils.py
AndreaGuarracino
2021-01-06
Pubseq fetch: sometimes a request times out. So repeat with intervals.
Pjotr Prins
2021-01-05
Add extra tab to display all items
BonfaceKilz
2021-01-05
cleaning update-from-genbank.py; removed unused import from genbank-fetch-ids.py
AndreaGuarracino
2021-01-05
Pass extra param that contains all news items to the template
BonfaceKilz
* bh20simplewebuploader/main.py (send_home): Add extra all_items when rendering the template.
2021-01-05
cleaning genbank-fetch-ids.py
AndreaGuarracino
2021-01-05
Fetching fixes
Pjotr Prins
2021-01-05
Add option for fetching fasta
Pjotr Prins
2021-01-05
fetch: do a straight dump of the original record
Pjotr Prins
2021-01-05
fetches original metadata from PubSeq/Arvados
Pjotr Prins
2021-01-05
web: show https
Pjotr Prins
2021-01-05
api: more cleanup
Pjotr Prins
2021-01-05
API: fix returned record to include original metadata
Pjotr Prins
2021-01-05
Rename
Pjotr Prins
2021-01-04
mapping: no longer requires specimen file for genbank output
Pjotr Prins
2021-01-04
Removing refs. No point in guessing terms
Pjotr Prins
2021-01-04
mapping sample_species using regex
Pjotr Prins
2021-01-04
Started on normalization
Pjotr Prins
2021-01-03
genbank: specimen source
Pjotr Prins
2021-01-03
genbank: more or less complete. Need to add collection method
Pjotr Prins
2021-01-03
genbank: deal with host, sex and age
Pjotr Prins
2021-01-03
genbank: technology parsing
Pjotr Prins
2021-01-03
genbank: submitter info
Pjotr Prins
2021-01-03
genbank: get authors
Pjotr Prins
2021-01-03
Move reference code to different file so it does not break python
Pjotr Prins
2021-01-02
GenBank date parsing
Pjotr Prins
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