v1.16.1

What's Changed

• EVA-3681 - New process to override BioSamples created in NCBI by @tcezard in #224
• Allow accession to complete when there are SV duplicates in the source file by @tcezard in #225
• EVA-3681 - Allow overwrite and override mode to change existing values on samples by @tcezard in #226
• EVA-3681 Fix last updated by @tcezard in #227

Full Changelog: v1.16...v1.16.1

v1.16

What's Changed

• Actually keep the samples that were created by @tcezard in #213
• EVA-3604 - Add naming convention check by @tcezard in #214
• EVA-3632 - Fix validation output file renaming in SV and naming convention by @tcezard in #215
• EVA-3619 Install Vep version if not available by @nitin-ebi in #217
• EVA-3484 - Move the data/project directories to the eload directory by @tcezard in #216
• Fix Async upload to ENA by @tcezard in #218
• EVA-3650 - Run new statistic calculation step by @tcezard in #220
• EVA-3641 Specify the analysis only option correctly by @tcezard in #219
• Gzip open default to binary so force to text by @tcezard in #221
• Fix: ENA platform and Imputation attributes by @tcezard in #222
• Fix aggregation check by @tcezard in #223

Full Changelog: v1.15.8...v1.16

v1.15.8

What's Changed

• EVA-3533 - Initial version of an orchestrator for submission processing by @tcezard in #211
• Allow derive sample from multiple sample accessions by @tcezard in #210
• Open the VCF file manually when running sample check as pysam fails sometime by @tcezard in #209
• Check that VEP has been run correctly by @tcezard in #208
• EVA-3624: Refactor biosamples communicators into pyutils by @apriltuesday in #212

Full Changelog: v1.15.7...v1.15.8

v1.15.7

What's Changed

• EVA-3560: SLURM migration by @apriltuesday in #206
• Update the FTP parsing to cope with changes on ensembl FTP by @tcezard in #205
• Remove instance id from accessioning and clustering by @tcezard in #207

Full Changelog: v1.15.6...v1.15.7

v1.15.6

• Use NCBI eutils key whenever possible by @tcezard in #203
• New script to test sample ownership by @tcezard in #204

Full Changelog: v1.15.5...v1.15.6

v1.15.5

• Allow insert_new_assembly.py to insert a new taxonomy only

ingestion

• Wait for all the accessioning to be complete before ingesting accessioning report in the variant warehouse

v1.15.4

Validation

• Remove platform restriction and add experiment type value

Brokering

• confirm samples brokering using existing and novel sample names

ingestion QC

• Skip check for VEP if not run
• Fix remapping ingestion log file name

v1.15.3

• qc_submission support optional statistic calculation
• Improve collection date and geographic location check for pre-submitted samples

v1.15.2

• Ensure annotation & statistics calculation are run per analysis
• Update qc_submission to check the new split variant load logs

v1.15

Preparation

• Create a dummy assembly report when none exists for sequences

Validation

• Validate existing BioSamples

Brokering

• Allow the Link label to be the link if no label is provided
• New script to update Biosamples
• Pass single sequence accession to ENA

Ingestion

• Split variant load
• During variant remapping extract VCF file with taxonomy id
• Normalise VCF before accessioning/variant load
• Merge accessioning and variant load in a single nextflow workflow