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Freezeman#1

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ehenrion wants to merge 91 commits intomainc3g/monitor:mainfrom freezemanc3g/monitor:freezemanCopy head branch name to clipboard

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Commits

Commits on Feb 21, 2023

• First draft for freezeman integration to the monitor

  

  Edouard Henrion

  committed
  2466897

Commits on Mar 22, 2023

• Fixing the email tempaltes

  

  Edouard Henrion

  committed
  e22f272

• Merge branch 'main' of github.com:c3g/monitor into freezeman

  Show description for e60c2ae
  

  Edouard Henrion

  committed
  e60c2ae

• Adding path for freezeman run info files to watch

  

  freezeman-qc

  committed
  2b5acd7

• Updating outdir for debug profile

  

  freezeman-qc

  committed
  d8d3786

• Fixed typo in config

  

  freezeman-qc

  committed
  468237f

• updating path for testing assets

  

  freezeman-qc

  committed
  8aa2115

Commits on Mar 27, 2023

• Setting monitor for Freezeman LIMS !

  

  freezeman-qc

  committed
  dbd10a6

Commits on May 15, 2023

• Freezeman monitor - Illumina runs and MGI runs are now all watched

  

  freezeman-qc

  committed
  755013d

Commits on May 24, 2023

• garantjm dev branch, child process Mem issue

  Show description for d6a96ef
  garantjm

  committed
  d6a96ef

• Updating the email start groovy template

  

  freezeman-dev

  committed
  1a10400

Commits on May 25, 2023

• Email templates fixes and updates

  

  freezeman-qc

  committed
  b36951b

Commits on May 29, 2023

• MGI T7 - fixed used of flag files path from config

  

  freezeman-qc

  committed
  e97df46

• Clarity - fixing use of config for MGI T7 flag files

  

  freezeman-qc

  committed
  904f7f0

• Start working on freezeman ingestion

  

  freezeman-qc

  committed
  233e8bb

Commits on May 31, 2023

• Genpipes as submodules

  Show description for 9d8c01d
  garantjm

  committed
  9d8c01d

• Merge branch 'fzmn-child-process' into freezeman

  Show description for 76438d6
  garantjm

  committed
  76438d6

• Updating the freezemannIngestor script and its call bty the momitor

  

  freezeman-qc

  committed
  7926728

• Merge branch 'freezeman' of https://github.com/c3g/monitor into freezeman

  

  freezeman-qc

  committed
  c07ff80

• fix config

  

  freezeman-qc

  committed
  498c368

Commits on Jun 1, 2023

• Fix run dir for illumina runs

  

  freezeman-qc

  committed
  4ff597e

• Readme, .py arguments format

  Show description for e8bbc34
  garantjm

  committed
  e8bbc34

• Merge branch 'freezeman' into fzmn-child-process

  garantjm

  committed
  d9200e5

• Fix debug.db path in config

  

  freezeman-qc

  committed
  d87eca0

• Revision of argparser, include password prompt

  Show description for 37cc733
  garantjm

  committed
  37cc733

• Changed GenPipes submodule URL to a public accessible https

  garantjm

  committed
  db3b7f9

Commits on Jun 2, 2023

• Fixing ini for genpipes as well as email start template

  

  freezeman-qc

  committed
  ead990b

• Changing definition of custom_ini

  

  freezeman-qc

  committed
  5f3f032

Commits on Jun 4, 2023

• Fixes on emails & BeginRun

  

  freezeman-qc

  committed
  aa87985

• Resetting 'onstart' emails for debug profile

  

  freezeman-qc

  committed
  b53fc23

• Merge branch 'main' into freezeman

  Show description for 89d669d
  

  freezeman-qc

  committed
  89d669d

• Updated .gitmodules with specific 'run_processing' branch from genpipes

  

  freezeman-qc

  committed
  eca0e7a

• Add correct imports in clarity/launch.nf

  

  freezeman-qc

  committed
  2439862

Commits on Jun 7, 2023

• Update doc information

  Show description for f74e2d5
  garantjm

  committed
  f74e2d5

• GetGenpipes process removed

  garantjm

  committed
  3d1ec86

Commits on Jun 8, 2023

• few adkjustmens in config + other minor changes

  

  freezeman-qc

  committed
  919cbf1

• Merge branch 'freezeman' into fzmn-child-process

  garantjm

  committed
  7e7e45e

Commits on Jun 13, 2023

• Strengthen the parsing of the MultiQC json

  

  freezeman-qc

  committed
  3450580

Commits on Jun 15, 2023

• Corrected outdir in BeginRun

  

  freezeman-qc

  committed
  5015b75

• Merge branch 'freezeman' into fzmn-child-process

  garantjm

  committed
  955c4ad

Commits on Jun 16, 2023

• Add fzmn-child-process configs & ini

  Show description for 3df7551
  garantjm

  committed
  3df7551

Commits on Jun 28, 2023

• GenPipes submodules updated

  Show description for 0c2322d
  garantjm

  committed
  0c2322d

Commits on Jul 19, 2023

• GetGenpipes leftovers removed, validation report ssh key, more logs

  Show description for 86adf51
  garantjm

  committed
  86adf51

• Merge branch 'fzmn-child-process' into freezeman

  Show description for 2d191ed
  garantjm

  committed
  2d191ed

Commits on Jul 20, 2023

• Add key arg to summary upload & errorStrategy ignore for emails

  Show description for 3a35094
  garantjm

  committed
  3a35094

Commits on Aug 3, 2023

• FreezemanIngestor connect & auth fixed, new arguments

  Show description for 448f6b8
  garantjm

  committed
  448f6b8

Commits on Aug 16, 2023

• Freezeman runinfo file modifications

  Show description for c1e2877
  garantjm

  committed
  c1e2877

Commits on Aug 31, 2023

• GenPipes update for run validation json, error strategy handling, documentation

  Show description for 3f1f8b3
  garantjm

  committed
  3f1f8b3

Commits on Sep 7, 2023

• Clarity BeginRun fixed with new GenPipes submodule

  Show description for 708f3a5
  garantjm

  committed
  708f3a5

Commits on Oct 27, 2023

• Path changes towards dedicated freezeman-processing

  garantjm

  committed
  31b5e5a

Commits on Jan 18, 2024

• GenPipes RunProcessing fixes for T7

  Show description for 720cc53
  garantjm

  committed
  720cc53

Commits on Jan 24, 2024

• Update MultiQC module

  garantjm

  committed
  a99ee50

• Genome null length issue and tweaks for freezeman-qc

  garantjm

  committed
  2cf0b37

Commits on Jan 29, 2024

• Genomic database copy paste fix in genpipes

  garantjm

  committed
  8798783

Commits on Feb 5, 2024

• Duplicate genomic database fix in genpipes readset

  garantjm

  committed
  72376b8

Commits on Feb 8, 2024

• Ingestion in Freezeman

  Show description for 03d6ae1
  garantjm

  committed
  03d6ae1

Commits on Feb 19, 2024

• FreezemanIngest running, freezemanIngestor sending multiple Validation report at once, workDir in scratch space

  garantjm

  committed
  f933d17

Commits on Feb 21, 2024

• Commenting out support for HiseqX, Iseq1 & Iseq2

  Show description for 1cb85a3
  garantjm

  committed
  1cb85a3

Commits on Feb 26, 2024

• Add project_name to validation report for Freezeman ingestion and exit code to ingestor

  garantjm

  committed
  11f064b

Commits on Mar 18, 2024

• NovaseqX paths & channels added, genpipes supported

  garantjm

  committed
  a6d6dcf

• New MultiQC run validation reports directory on genap's datahub

  garantjm

  committed
  0a11418

• Reorder to have NovaseqX ready up before Novaseq

  Show description for 8cf5aea
  garantjm

  committed
  8cf5aea

Commits on Mar 20, 2024

• NovaseqX flowcell string has a different position in path

  Show description for bbb3afd
  garantjm

  committed
  bbb3afd

Commits on Mar 27, 2024

• Run_processing relies on GenPipes version of adapter_settings_format.txt

  garantjm

  committed
  bd866bf

• Repair profiles string in config

  garantjm

  committed
  0de8621

• Update MulitQC, add year to outdir path & clean logs

  garantjm

  committed
  5f3973d

• NovaseqX index job, WGBS not aligned, summaryReport T7

  garantjm

  committed
  104b779

Commits on Apr 1, 2024

• Add year to monitor.nf watchPath

  garantjm

  committed
  1f9c54c

Commits on Apr 4, 2024

• HotFix: params.outdir set instead of .mgi.outdir

  garantjm

  committed
  15478a9

Commits on Apr 22, 2024

• Genpipes run_validation report with url towards datahub Freezeman_validation folder

  garantjm

  committed
  50265e3

• Fix validation report URL in finish email template, update onfinish email list

  garantjm

  committed
  1584bd3

Commits on Apr 25, 2024

• GenPipes copy step includes a compression job of logs.

  garantjm

  committed
  cfe5661

Commits on May 16, 2024

• Update mugqic_tools to fix types in alignment metrics for run validation

  garantjm

  committed
  8ef1d85

Commits on Jul 4, 2024

• Folder name added to finish email

  Show description for 15dfcd4
  garantjm

  committed
  15dfcd4

Commits on Jul 11, 2024

• Replace run value from MultiQC with run_name from run info file, add the start email table

  garantjm

  committed
  6de729b

Commits on Jul 15, 2024

• Simple copy of each MultiQC run to the run processing folder

  garantjm

  committed
  2afac82

Commits on Aug 29, 2024

• Includes QoL changes requested by the lab

  Show description for cc2a78e
  garantjm

  committed
  cc2a78e

Commits on Oct 24, 2024

• Sex concordance fix and new certificates

  garantjm

  committed
  a6089ab

Commits on Oct 28, 2024

• Remove retries for BeginRun to make sure there are no double launches on qsub failures

  garantjm

  committed
  8a184fc

Commits on Nov 4, 2024

• Update MultiQC_C3G to v1.23

  garantjm

  committed
  d63efb3

Commits on Nov 14, 2024

• Update indexes, barcodes, adapters in GenPipes

  garantjm

  committed
  0059dea

Commits on Dec 3, 2024

• Add sortmerna for RNAseq reports

  garantjm

  committed
  f4b3322

Commits on Dec 5, 2024

• Removing retries to reduce the potential issues associated

  garantjm

  committed
  8ad8536

• Merge sortmerna & copy step PR in GenPipes

  garantjm

  committed
  8f79f81

Commits on Dec 11, 2024

• Genpipes fix for Danielle missing mkdir in fastq move

  garantjm

  committed
  84aa070

• Change the glob expression that ignores dnbseqt7 for a glob restricted to novaseqs sequencers

  garantjm

  committed
  e34b5e2

Commits on Dec 16, 2024

• Adding Ioannis Ragoussis to emailonfinish list

  garantjm

  committed
  2cb2f87

Commits on Dec 18, 2024

• MultiQC reports rsynced towards /lb/robot/ as well as /nb/Research

  garantjm

  committed
  23ec915

• update genpipes version within monitor

  Show description for 3976ff7
  MareikeJaniak

  committed
  3976ff7

• add curl command to send data to dashrunr after multiqc report is generated

  MareikeJaniak

  committed
  592dfc1

Commits on Dec 19, 2024

• update genpipes version within monitor

  MareikeJaniak

  committed
  233a033