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Xoco #5

Merged
merged 31 commits into from
Sep 24, 2022
Merged

Xoco #5

merged 31 commits into from
Sep 24, 2022

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scunnac
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@scunnac scunnac commented Sep 24, 2022

  • updated documentation
  • implemented an automatic download of latest singularity containers (guppy 6.7.3) with https URL of files on Drive IRD
  • read id list for splitting fast5 files into genome bins is now created with the R script that handles creating genome specific fastq files. Hopefully, this solve occasional problems with fast5_subset from the ont api that failled because of supposedly too long read names.
  • python scripts interface clarified between slurm and cluster. Documentation indicate that only local and slurm modes will be kept for configure

@scunnac
Implement mode slurm in the CLI
6f6b7a1
@scunnac
Implement mode slurm in the CLI
9aa0798
@scunnac
Implement mode slurm in the CLI
bac0451
@scunnac
upgrade a bunch of UNTESTED env files
a10bae6
@scunnac
Include a new 'bigger' test read fast5 dataset
b2d9fca
@scunnac
UNTESTED changes to fix important bugs
896325d
@scunnac
more update
2679e0f
@scunnac
more test reads fast5 files
3afb48f
@scunnac
close to have a new version working locally with latest sing files
878e1c9
@scunnac
new deepbinner sif file TO BE TESTED
7bb8d43
@scunnac
works in basic tests
977d8e5
@scunnac
works in few more tests
ffc02bc
@scunnac
move slumr dir up one level
be91f39
@scunnac
updating the slurm profile from https://github.com/Snakemake-Profile
089bad4
@scunnac
includes Singularity UNTESTED
fa03a94
@scunnac
improved and updated
02f6d15
@scunnac
typos
610f6c1
@scunnac
images on Drive and squeeze messages
c150877
@scunnac
fix squeeze
b023943
@scunnac
perso_notes
be79c6b
@scunnac
this works in simple tests on iTrop with slurm
ed500c5
@scunnac
sould corrects log path in sbatch script for rule report_demultiplex
9854af9
@scunnac
Revert "sould corrects log path in sbatch script for rule report_demu…
bbf5c04 
…ltiplex"

This reverts commit 9854af9
@scunnac
Revert "Revert "sould corrects log path in sbatch script for rule rep…
ed883c8 
…ort_demultiplex""

This reverts commit bbf5c04
@scunnac
sould correct: Resources values have to be integers, strings, or call…
b0b2e7c 
…ables (functions)
@scunnac
sould correct: Resources values have to be integers, strings, or call…
188445c 
…ables (functions)
@scunnac
remove resource spec in basecall to see if it solves couda_invalid_de…
c89a5ed 
…vice
@scunnac
remove basecall output dir content if it exists...
000f56f
@scunnac
fix log for cluster config in report demultiplex
2252395
@scunnac
config on iTrop with slurm that worked with the test dataset
4c78628
@scunnac
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scunnac commented Sep 24, 2022

Tested with sample data set on a laptop and on iTrop with both local and slurm mode

@scunnac scunnac closed this Sep 24, 2022
@scunnac scunnac reopened this Sep 24, 2022
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scunnac commented Sep 24, 2022

Good to go

@scunnac scunnac merged commit a4413eb into master Sep 24, 2022
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@scunnac