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AgeCommit message (Expand)Author
2021-03-17Use default output of pipelinegenerate-cwlArun Isaac
2021-03-17Do not specify outputs to be of File type.Arun Isaac
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
2020-12-31genbank: moving script into workflow spacePjotr Prins
2020-12-30IgnoresPjotr Prins
2020-12-30Genbank: commentsPjotr Prins
2020-11-21added abPOA workflow; typosAndreaGuarracino
2020-11-15removed provider_sample_id referencesAndreaGuarracino
2020-11-15fix sequencing_coverageAndreaGuarracino
2020-11-15fixed typos in the integer castAndreaGuarracino
2020-11-15added a check on host_ageAndreaGuarracino
2020-11-14added a check on host_ageAndreaGuarracino
2020-11-14check empty stringsAndreaGuarracino
2020-11-13fix check date sra scriptAndreaGuarracino
2020-11-13generation of dates a little more robustAndreaGuarracino
2020-11-13to not create YAML files with date before 2019 DecemberAndreaGuarracino
2020-11-13fix in the ids to considerAndreaGuarracino
2020-11-13added ids-to-consider option to the NCBI scriptAndreaGuarracino
2020-11-12managed the assembly_method in the scripts, doc, and the example templatesAndreaGuarracino
2020-11-12updated alignment_protocol field in the script, doc, and the example templatesAndreaGuarracino
2020-11-11Conflict in guix-deployPjotr Prins
2020-11-11DeploymentPjotr Prins
2020-11-11Move files to correct folderlltommy
2020-11-11Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-11-11Adding covid death and covid cases per country as additional background infor...lltommy
2020-11-11create_sra_metadata script doesn't trick the quality control about missing da...AndreaGuarracino
2020-11-10virtuoso: no-cachePjotr Prins
2020-11-10virtuoso: header changePjotr Prins
2020-11-10virtuoso: Added a --no-cache optionPjotr Prins
2020-11-08Uploaded UTHSC sequencesPjotr Prins
2020-11-08UTHSC samplesPjotr Prins
2020-11-06Add country entries that miss coordinatesPjotr Prins
2020-11-06Country trouble shootingPjotr Prins
2020-11-06CountriesPjotr Prins
2020-11-06Using correct wikidata geo linkPjotr Prins
2020-11-06Adding Tennessee itemsPjotr Prins
2020-11-06UTHSC upload infoPjotr Prins
2020-09-29esr_samples script refactoring; added a reference of the esr_samples script i...AndreaGuarracino
2020-09-28new countries; updated genbank/sra scripts to manage more specimen sourcesAndreaGuarracino
2020-09-28genbank and sra scripts more picky on the ontologies; added utils.py for shar...AndreaGuarracino
2020-09-27Virtuoso uploader: instructionsPjotr Prins
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