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2021-03-17Do not specify inputs to be of File type.Arun Isaac
2021-03-07Rewrite fastq2fasta.scm using new ccwl APIArun Isaac
2021-03-07Implement bowtie, bwa-mem variant calling in ccwlArun Isaac
2021-02-25Rewrite fastq2fasta workflow using clitool-stepArun Isaac
2021-02-25Move generate-cwl to its own repositoryArun Isaac
2021-02-21Implement fastq2fasta workflows in schemeArun Isaac
2021-02-21Add CWL generator for Workflow workflowsArun Isaac
2021-02-21Add CWL generator for CommandLineTool workflowsArun Isaac
2021-02-21Add a scm->yaml generatorArun Isaac
2021-01-28Jetson test sequenceHEADmasterPjotr Prins
2021-01-28Restored tools submodulePjotr Prins
2021-01-28Moving tools out of submodules (sorry!)Pjotr Prins
2021-01-28Adding support for AuspicePjotr Prins
2021-01-26Merge pull request #124 from urbanslug/masterPjotr Prins
Add phylogeny workflow
2021-01-26Add phylogeny workflowNjagi Mwaniki
Signed-off-by: Njagi Mwaniki <njagi@urbanslug.com>
2021-01-08GenBank: Fix normalization and depth differences with original recordsPjotr Prins
2021-01-08Set JSON indentationPjotr Prins
2021-01-08Get correct GenBank ID with version, see #122Pjotr Prins
2021-01-08FASTA file should not have leading spacePjotr Prins
2021-01-07fixed comments in the example yaml filesAndreaGuarracino
2021-01-07Merge pull request #121 from BonfaceKilz/chore/add-extra-tab-for-all-feedsPjotr Prins
Chore/add extra tab for all feeds
2021-01-07Allow for xml and xml.gz filesPjotr Prins
2021-01-06cleaned utils.pyAndreaGuarracino
2021-01-06Pubseq fetch: sometimes a request times out. So repeat with intervals.Pjotr Prins
2021-01-05Add extra tab to display all itemsBonfaceKilz
2021-01-05cleaning update-from-genbank.py; removed unused import from genbank-fetch-ids.pyAndreaGuarracino
2021-01-05Pass extra param that contains all news items to the templateBonfaceKilz
* bh20simplewebuploader/main.py (send_home): Add extra all_items when rendering the template.
2021-01-05cleaning genbank-fetch-ids.pyAndreaGuarracino
2021-01-05Fetching fixesPjotr Prins
2021-01-05Add option for fetching fastaPjotr Prins
2021-01-05fetch: do a straight dump of the original recordPjotr Prins
2021-01-05fetches original metadata from PubSeq/ArvadosPjotr Prins
2021-01-05web: show httpsPjotr Prins
2021-01-05api: more cleanupPjotr Prins
2021-01-05API: fix returned record to include original metadataPjotr Prins
2021-01-05RenamePjotr Prins
2021-01-04mapping: no longer requires specimen file for genbank outputPjotr Prins
2021-01-04Removing refs. No point in guessing termsPjotr Prins
2021-01-04mapping sample_species using regexPjotr Prins
2021-01-04Started on normalizationPjotr Prins
2021-01-03genbank: specimen sourcePjotr Prins
2021-01-03genbank: more or less complete. Need to add collection methodPjotr Prins
2021-01-03genbank: deal with host, sex and agePjotr Prins
2021-01-03genbank: technology parsingPjotr Prins
2021-01-03genbank: submitter infoPjotr Prins
2021-01-03genbank: get authorsPjotr Prins
2021-01-03Move reference code to different file so it does not break pythonPjotr Prins
2021-01-02GenBank date parsingPjotr Prins
2021-01-02transform-genbank-xml2yamlfa.py refactoringPjotr Prins
2021-01-02transform-genbank-xml2yamlfa.py rewritePjotr Prins
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