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Vm ww viloca automation#17

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Commits

Commits on Jun 8, 2023

• [WIP] initial restructuring from S3C

  

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• wastewater-only modifications

  

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Commits on Sep 28, 2023

• First version of VM-based wastewater automationw

  

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Commits on Oct 3, 2023

• VM automation + viloca autorun

  

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• production Dockerfile

  

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Commits on Oct 4, 2023

• mirrors now reside on Euler

  

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• sort samples relies on Euler downloads

  

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Commits on Oct 5, 2023

• added storing names of processed batches for uploader

  

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• [FIX] partial fix FGCZ connection

  

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• [FIX] upload call

  

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Commits on Nov 6, 2023

• [WIP] new euler-based architecture

  

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• [WIP] sync fix

  

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• fix sync_fgcz batman

  

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• cleanup

  

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• fix conda

  

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• fix batman vars

  

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• [WIP] paths fix

  

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• fix conda

  

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Commits on Nov 7, 2023

• sync setup

  

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• fix viloca

  

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Commits on Nov 8, 2023

• development

  

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Commits on Nov 9, 2023

• debugging configuration

  

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Commits on Nov 13, 2023

• [WIP] uploader migration

  

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• uploader migration

  

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• uploader - cleanup

  

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  74ed6d8

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• fix paths

  

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• fix sync

  

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• fix regular expression

  

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• fix config

  

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Commits on Nov 14, 2023

• fix batch check

  

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• activate duplicate check

  

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• fix movedatafiles

  

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• add quotas for uploader

  

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• removed debug entrypoint

  

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Commits on Nov 15, 2023

• bug fixes

  

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• fix paths

  

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• disable mail

  

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• including migration to slurm

  

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• fix batman.sh functions

  

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• fix movedatafiles

  

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Commits on Nov 16, 2023

• Merging latest master into VM branch

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Commits on Nov 20, 2023

• updated paths

  

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• fix paths

  

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• fix configuration

  

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• fix paths

  

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• fix configuration

  

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• detangled backup from processing

  

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• moving queue_uploads remotely

  

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Commits on Nov 22, 2023

• status tracking bug fixes

  

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Commits on Nov 23, 2023

• fix viloca paths

  

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Commits on Nov 24, 2023

• bug fix viloca

  

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• bug fix run detection VILOCA

  

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• multiple fixes uploader code

  

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Commits on Dec 1, 2023

• update uploader paths

  

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• updated uploader variables

  

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• added listing viloca samples

  

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• added completion check and rerun VILOCA

  

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Commits on Dec 4, 2023

• fixed viloca status tracking

  

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Commits on Dec 6, 2023

• add amplicon_coverage step

  

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• added conda environment yaml files

  

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• fix amplicon cov paths

  

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• fix typo

  

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• fix typo

  

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• restore container functionality after testing

  

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• added manual amplicon_cov options

  

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• fix paths

  

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• fix manual amplicon_cov functions

  

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• removing unused loop

  

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• fix variables

  

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• adapting carillon to new amplicon cov syntax

  

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• fix typo

  

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Commits on Dec 7, 2023

• renamed status files for clarity

  

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• adding hostname to sync output

  

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Commits on Dec 8, 2023

• fix directories viloca

  

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Commits on Dec 15, 2023

• implemented uploader at VM level

  

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Commits on Dec 18, 2023

• [WIP] uploader metadata fixes

  

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Commits on Jan 18, 2024

• - added backup system on BSSE folder

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• cleanup viloca command

  

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• bug fixes viloca run

  

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Commits on Feb 5, 2024

• backups setup and fixes

  

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• [fix] exception for malformed json stat files

  

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• activate backups

  

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• fix amplicon cov backup status test

  

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• fix viloca restart logic

  

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Commits on Feb 7, 2024

• bug fixes

  

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Commits on Feb 8, 2024

• Documentation of VM annotation

  

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Commits on Feb 9, 2024

• add reproducibility information to statusfiles

  

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• pangolin version and output saved to log files

  

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Commits on Feb 19, 2024

• fix uploader strain name building

  

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Commits on Feb 29, 2024

• bug fixes

  

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Commits on Mar 5, 2024

• updating settings

  

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• fix batman amplicon_coverage

  

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Commits on Mar 11, 2024

• update blacklist

  

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• bug fix on parsing older sample names

  

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Commits on Mar 26, 2024

• added processing of project p34560

  

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Commits on Apr 2, 2024

• added blacklisting to uploader

  

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Commits on Apr 8, 2024

• update configuration

  

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Commits on Apr 15, 2024

• add full year processing commands

  

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Commits on May 13, 2024

• update settings

  

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Commits on May 14, 2024

• [FIX] adapt to new FGCZ filename conventions

  

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• [FIX] adapt to new FGCZ filenames

  

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• [FIX] fixing FGCZ filename changes

  

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• [FIX] fixed uploader switch

  

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Commits on May 23, 2024

• [FEAT] added blacklist for uploader

  

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Commits on Jun 12, 2024

• [FEAT] ftp/https fgcz sync choice

  

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• [FEAT] aviti sequencing conditional

  

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Commits on Jun 26, 2024

• [WIP] aviti automation changes

  

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• [FIX] uploader does not attempt uploads if no sample is available after removing blacklisted items

  

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Commits on Jul 3, 2024

• [FEAT] sortsamples for Aviti sequencing

  

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• [FIX] aviti sequencing

  

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Commits on Jul 8, 2024

• [FEAT] branching automation for Aviti sequencing

  

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Commits on Jul 10, 2024

• [FIX] https/ftp download fix

  

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• [FIX] fix ftp/https switch

  

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• [FIX] fix conditional stopping uploads for empty submissions

  

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Commits on Jul 23, 2024

• [FIX] restore FTP downloads with new folder structure

  

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Commits on Aug 12, 2024

• [FIX] bug fix --recent option

  

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• [FIX] bug fixing

  

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Commits on Oct 28, 2024

• [FEAT] aviti processing

  

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Commits on Jan 7, 2025

• [FEAT] adapted to new separate fgcz downloader

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• [FEAT] automated archival of cram files from Euler to wisedb

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