Ecosyste.ms: Issues

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GitHub / BU-ISCIII/relecov-tools issues and pull requests

#231 - Changes in schemas to simplify map_schema.py and to fix missing ontologies

Pull Request - State: closed - Opened by Shettland over 1 year ago - 1 comment

#227 - Fixed read_lab_metadata.py to handle errors like missing data

Pull Request - State: closed - Opened by Shettland over 1 year ago

#226 - Introduced new options to download function

Pull Request - State: closed - Opened by Shettland almost 2 years ago - 5 comments

#225 - fixed error when sending several parameters via API

Pull Request - State: closed - Opened by luissian about 2 years ago

#224 - Minor fixes feed database

Pull Request - State: closed - Opened by saramonzon about 2 years ago

#223 - fix label for variant designation in schema

Pull Request - State: closed - Opened by saramonzon about 2 years ago

#222 - Reviewing and fixing Bioinfo metadata module

Pull Request - State: closed - Opened by saramonzon about 2 years ago

#221 - Included collecting_institution, secuencing_data, GISAID and ENA fiel…

Pull Request - State: closed - Opened by luissian about 2 years ago

#219 - Fixes and changes in validate module

Pull Request - State: closed - Opened by saramonzon about 2 years ago

#218 - remove the self.headers in the PUT request

Pull Request - State: closed - Opened by luissian about 2 years ago

#217 - Comments and some fixes

Pull Request - State: closed - Opened by saramonzon about 2 years ago - 1 comment

#216 - fixed issue 215

Pull Request - State: closed - Opened by luissian about 2 years ago

#215 - Invalid " table" field for "host subject id" and "study_type"

Issue - State: closed - Opened by luissian about 2 years ago
Labels: bug

#214 - fixed bug in long parse because changes in configuration json

Pull Request - State: closed - Opened by luissian about 2 years ago

#213 - Changes in gisaid metadata (gisaid_upload.py, relecov and gisaid schemas)

Pull Request - State: closed - Opened by mlarjim about 2 years ago

#212 - changes in gisaid_upload, __main__ and config json

Pull Request - State: closed - Opened by mlarjim about 2 years ago

#211 - Actualizado el read bioinfo metadata y mas

Pull Request - State: closed - Opened by luissian about 2 years ago

#210 - ena_schema.json vs relecov_schema.json y ena-upload-cli

Pull Request - State: closed - Opened by ErikaKvalem about 2 years ago

#209 - added geo_loc region and purpose for sequencing

Pull Request - State: closed - Opened by luissian about 2 years ago

#208 - Review ena schema vs ena upload cli and relecov schema

Pull Request - State: closed - Opened by ErikaKvalem about 2 years ago

#206 - Changed anatomical_material_config.json & collection device

Pull Request - State: closed - Opened by ErikaKvalem about 2 years ago

#205 - changes in relecov schema and convert float to string

Pull Request - State: closed - Opened by luissian about 2 years ago

#204 - Fixing ISCIII.py

Pull Request - State: closed - Opened by ErikaKvalem about 2 years ago

#203 - Change configuration json hierarchy

Pull Request - State: closed - Opened by ErikaKvalem about 2 years ago

#202 - changes in read lab metadata, homogenizer and schema .

Pull Request - State: closed - Opened by luissian about 2 years ago

#201 - Added rename function to ena upload

Pull Request - State: closed - Opened by ErikaKvalem about 2 years ago

#200 - ENA upload working on functions

Pull Request - State: closed - Opened by ErikaKvalem about 2 years ago

#199 - created processed json but without valid enum

Pull Request - State: closed - Opened by luissian about 2 years ago

#198 - Fixed terms to configuration json

Pull Request - State: closed - Opened by ErikaKvalem about 2 years ago

#197 - fixed bug in homgenizer

Pull Request - State: closed - Opened by luissian about 2 years ago

#196 - Ontology review

Pull Request - State: closed - Opened by Alema91 about 2 years ago

#195 - Fixing schema anatomical material

Pull Request - State: closed - Opened by ErikaKvalem about 2 years ago

#194 - Small changes relecov schema

Pull Request - State: closed - Opened by ErikaKvalem about 2 years ago

#193 - modify excel heading and do not set Environmental System to swab

Pull Request - State: closed - Opened by luissian about 2 years ago

#191 - Adding changes in relecov schema y xlsx

Pull Request - State: closed - Opened by ErikaKvalem about 2 years ago

#190 - Changes in ISCIII.json schema

Issue - State: closed - Opened by saramonzon about 2 years ago

#189 - Incorrect string value: '\xE2\x80\x91CoV...

Pull Request - State: closed - Opened by luissian about 2 years ago

#188 - Fixing schemas

Pull Request - State: closed - Opened by ErikaKvalem about 2 years ago

#187 - Changes in relecov schema

Pull Request - State: closed - Opened by ErikaKvalem about 2 years ago

#186 - Changes in schema relecov

Pull Request - State: closed - Opened by ErikaKvalem about 2 years ago

#185 - Fixing relecov schema

Pull Request - State: closed - Opened by ErikaKvalem about 2 years ago

#184 - fixed issue 183

Pull Request - State: closed - Opened by luissian about 2 years ago

#183 - json output from long_table_parse module is not

Issue - State: closed - Opened by luissian about 2 years ago - 1 comment
Labels: bug

#182 - Fixes relecov schema v1.0.0

Pull Request - State: closed - Opened by saramonzon about 2 years ago

#181 - modified long_table_parse.py, changed sample to sample_name

Pull Request - State: closed - Opened by luisiJavo over 2 years ago

#180 - fixed relecov_tools/feed_database.py, deleted pdb

Pull Request - State: closed - Opened by luisiJavo over 2 years ago

#179 - change the bioinfo json to list of samples

Pull Request - State: closed - Opened by luissian over 2 years ago

#178 - Improved GISAID upload

Pull Request - State: closed - Opened by mlarjim over 2 years ago

#177 - Corrected parse variant_long_table.csv ->nucleotide -> alt

Pull Request - State: closed - Opened by luisiJavo over 2 years ago

#176 - allow to continue uploading sample if the sample is already defined

Pull Request - State: closed - Opened by luissian over 2 years ago

#175 - Added broker_name to experiment.xml, run.xml and submission.xml

Pull Request - State: closed - Opened by ErikaKvalem over 2 years ago

#174 - Small changes in examples

Pull Request - State: closed - Opened by ErikaKvalem over 2 years ago

#173 - including schema_name and schema_version at feed_database for relecov

Pull Request - State: closed - Opened by luissian over 2 years ago

#172 - Added regex function for md5sum

Pull Request - State: closed - Opened by ErikaKvalem over 2 years ago

#171 - Include schema name and schema version in read_lab and bioinfo metadata

Pull Request - State: closed - Opened by luissian over 2 years ago

#170 - Changed names in bioinfo metadata lab

Pull Request - State: closed - Opened by ErikaKvalem over 2 years ago

#169 - Added templates folder and files

Pull Request - State: closed - Opened by ErikaKvalem over 2 years ago

#167 - Updated homogenizer, added user/passwd on sftp and fixed minor issues

Pull Request - State: closed - Opened by luissian over 2 years ago

#166 - Changes in relecov schema and ena schema

Pull Request - State: closed - Opened by ErikaKvalem over 2 years ago

#165 - Minor changes in array coordenates

Pull Request - State: closed - Opened by Alema91 over 2 years ago

#164 - Field name change

Pull Request - State: closed - Opened by ErikaKvalem over 2 years ago

#161 - Changes in format bioinfo

Pull Request - State: closed - Opened by Alema91 over 2 years ago

#160 - Adding options for sequencing instrument platform

Pull Request - State: closed - Opened by ErikaKvalem over 2 years ago

#159 - handling additional files for metadata_homogenizer module

Pull Request - State: closed - Opened by luissian over 2 years ago

#158 - Adding CHECKLIST to sample.xml

Pull Request - State: closed - Opened by ErikaKvalem over 2 years ago

#157 - Updated GISAID schema and changes in gisaid_upload

Pull Request - State: closed - Opened by mlarjim over 2 years ago

#156 - Changes for batch upload

Pull Request - State: closed - Opened by ErikaKvalem over 2 years ago

#155 - changes in read lab metadata for ENA ,and added new lab in config

Pull Request - State: closed - Opened by luissian over 2 years ago

#154 - Invalid metadata file contains all samples including valid ones

Issue - State: closed - Opened by luissian over 2 years ago
Labels: bug

#153 - implemented issue 152

Pull Request - State: closed - Opened by luissian over 2 years ago

#152 - Metadata mapping cannot field dummy info for run alias

Issue - State: closed - Opened by luissian over 2 years ago - 1 comment
Labels: bug

#151 - Update homogenizer module do not add additional fields

Issue - State: closed - Opened by luissian over 2 years ago - 1 comment
Labels: bug

#150 - Working on read_lab_metadata

Pull Request - State: closed - Opened by ErikaKvalem over 2 years ago

#149 - Added funcionality to correct R2 checksum

Pull Request - State: closed - Opened by ErikaKvalem over 2 years ago

#148 - Resolved: R1.fastq & R2.fastq had the same md5 checksum

Pull Request - State: closed - Opened by mlarjim over 2 years ago

#147 - Updated the homogenizer module and laboratories

Pull Request - State: closed - Opened by luissian over 2 years ago

#97 - upload to bioinfo analysis json to Relecov-plaform

Issue - State: closed - Opened by luissian over 2 years ago
Labels: enhancement

#96 - Upload 96 sample s to iSkyLIMS

Issue - State: closed - Opened by luissian over 2 years ago
Labels: enhancement

#93 - modify feed_database to be used for sending analysis/longtable info to relecov-platform

Issue - State: closed - Opened by luissian over 2 years ago
Labels: enhancement

#88 - Create first version of relecov-tool in oficial repo pypi.org

Issue - State: closed - Opened by luissian over 2 years ago - 1 comment

#80 - Descargar secuencias y metadata de GISAID 3800 secuencias

Issue - State: closed - Opened by ErikaKvalem over 2 years ago - 1 comment

#69 - Upload 96 samples

Issue - State: closed - Opened by ErikaKvalem over 2 years ago - 11 comments

#68 - Add to ena_upload.py how we introduce column names for dataframe creation

Issue - State: closed - Opened by ErikaKvalem over 2 years ago
Labels: enhancement

#50 - Launch module

Issue - State: closed - Opened by saramonzon over 2 years ago

#48 - Read metadata for bioinfo data

Issue - State: closed - Opened by saramonzon over 2 years ago - 9 comments

#46 - Script to upload to gisaid

Issue - State: closed - Opened by saramonzon over 2 years ago