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Freezeman #1

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@ehenrion ehenrion commented Jun 4, 2023

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Edouard Henrion and others added 30 commits February 21, 2023 10:39
First draft for freezeman integration to the monitor
2466897
Fixing the email tempaltes
e22f272
Merge branch 'main' of github.com:c3g/monitor into freezeman
e60c2ae 
Conflicts:
	workflows/mgi/monitor.nf
	workflows/testing.nf
Adding path for freezeman run info files to watch
2b5acd7
Updating outdir for debug profile
d8d3786
Fixed typo in config
468237f
updating path for testing assets
8aa2115
Setting monitor for Freezeman LIMS !
dbd10a6
Freezeman monitor - Illumina runs and MGI runs are now all watched
755013d
@garantjm
garantjm dev branch, child process Mem issue
d6a96ef 
First attempt at a correction of the monitor memory overuse issue. Hypothesis: Stopping the monitor desn't kill the child processes and the stop'n'launch of debugging increases the amount of loose child processes that hug the memory.
Updating the email start groovy template
1a10400
Email templates fixes and updates
b36951b
MGI T7 - fixed used of flag files path from config
e97df46
Clarity - fixing use of config for MGI T7 flag files
904f7f0
Start working on freezeman ingestion
233e8bb
@garantjm
Genpipes as submodules
9d8c01d 
The monitor calls a process to clone or link genpipes for each channel instances, it shouldn't even be a process
@garantjm
Merge branch 'fzmn-child-process' into freezeman
76438d6 
Conflicts:
	workflows/freezeman/monitor.nf
Updating the freezemannIngestor script and its call bty the momitor
7926728
Merge branch 'freezeman' of https://github.com/c3g/monitor into freez…
c07ff80 
…eman
fix config
498c368
Fix run dir for illumina runs
4ff597e
@garantjm
Readme, .py arguments format
e8bbc34 
Include a first version of a README, modification of arguments in freezemanIngestor.py to a more common format
@garantjm
Merge branch 'freezeman' into fzmn-child-process
d9200e5
Fix debug.db path in config
d87eca0
@garantjm
Revision of argparser, include password prompt
37cc733 
Positional argument for JSON, inclusion of metavar, option to have password prompt and redirection of else error message to stderr
@garantjm
Changed GenPipes submodule URL to a public accessible https
db3b7f9
Fixing ini for genpipes as well as email start template
ead990b
Changing definition of custom_ini
5f3f032
Fixes on emails & BeginRun
aa87985
Resetting 'onstart' emails for debug profile
b53fc23
garantjm and others added 21 commits April 22, 2024 14:39
@garantjm
Fix validation report URL in finish email template, update onfinish e…
1584bd3 
…mail list
@garantjm
GenPipes copy step includes a compression job of logs.
cfe5661
@garantjm
Update mugqic_tools to fix types in alignment metrics for run validation
8ef1d85
@garantjm
Folder name added to finish email
15dfcd4 
Requested by Janick St-Cyr for her convenience
@garantjm
Replace run value from MultiQC with run_name from run info file, add …
6de729b 
…the start email table
@garantjm
Simple copy of each MultiQC run to the run processing folder
2afac82
@garantjm
Includes QoL changes requested by the lab
cc2a78e 
Includes a fix for the tar compression to ignore its own outputs and removing the MultiQC .html from email attachments
@garantjm
Sex concordance fix and new certificates
a6089ab
@garantjm
Remove retries for BeginRun to make sure there are no double launches…
8a184fc 
… on qsub failures
@garantjm
Update MultiQC_C3G to v1.23
d63efb3
@garantjm
Update indexes, barcodes, adapters in GenPipes
0059dea
@garantjm
Add sortmerna for RNAseq reports
f4b3322
@garantjm
Removing retries to reduce the potential issues associated
8ad8536
@garantjm
Merge sortmerna & copy step PR in GenPipes
8f79f81
@garantjm
Genpipes fix for Danielle missing mkdir in fastq move
84aa070
@garantjm
Change the glob expression that ignores dnbseqt7 for a glob restricte…
e34b5e2 
…d to novaseqs sequencers
@garantjm
Adding Ioannis Ragoussis to emailonfinish list
2cb2f87
@garantjm
MultiQC reports rsynced towards /lb/robot/ as well as /nb/Research
23ec915
@MareikeJaniak
update genpipes version within monitor
3976ff7 
throttling fixes, bam names unique
@MareikeJaniak
add curl command to send data to dashrunr after multiqc report is gen…
592dfc1 
…erated
@MareikeJaniak
update genpipes version within monitor
233a033
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@ehenrion @garantjm @MareikeJaniak