BU-ISCIII/buisciii-tools

Issues

• New-services's MD5 verification checks all the reads from a project

  #362 opened 2 months ago by victor5lm
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• Add alberto.campoy to sftp_user.json

  #361 opened 2 months ago by victor5lm
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• FASTQ integrity check to be added to new-service tool

  #319 opened 2 months ago by juanledesma78
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• Fix-permissions module does not allow for multiple arguments

  #348 opened 2 months ago by victor5lm
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• Wrong singularity cache directory in taxprofiler.config

  #349 opened 2 months ago by victor5lm
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• Fix remove_columns_mapping_table.sh script

  #350 opened 2 months ago by svarona
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• BUG Error string in except

  #352 opened 2 months ago by saramonzon
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• Update mtbseq version

  #354 opened 2 months ago by victor5lm
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• Add jmgonzalez to sftp_user.json

  #355 opened 2 months ago by victor5lm
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• Remove conda env line from viralrecon's results lablog

  #357 opened 2 months ago by victor5lm
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• MTBSeq template: no headers added in 03-mtbseq lablog

  #342 opened 3 months ago by Shettland
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• Wrong SFTP credentials in delivery email

  #353 opened 2 months ago by svarona
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• Improve broken symlink handling in excel_generator.py

  #242 opened 3 months ago by Shettland
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• Bioinfo-doc does not offer to use txt file for email notes if not given for delivery notes

  #326 opened 3 months ago by Shettland
  1

• Missing sftp folder in sftp_user.json

  #343 opened 3 months ago by Shettland
  0

• Update sarek version and config in the exome templates

  #340 opened 3 months ago by victor5lm
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• Latest MAG version uses .csv samplesheet as input instead of .fastq.gz files

  #333 opened 3 months ago by victor5lm
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• Bioinfo-doc does not apply indentations in the email notes

  #308 opened 5 months ago by victor5lm
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• Kraken save_no_host config saves both unclassified and classified reads and files

  #312 opened 4 months ago by svarona
  2

• Update release version tag in __main__

  #313 opened 4 months ago by Shettland
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• Error when profile_classification_area is missing

  #314 opened 4 months ago by Shettland
  2

• Outdated pipeline version in RNASEQ template

  #315 opened 4 months ago by Shettland
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• Change incorrect path in characterization template

  #322 opened 4 months ago by Shettland
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• Update ariba singularity image in characterization/REFERENCES

  #323 opened 4 months ago by Shettland
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• Include MLVA template

  #324 opened 4 months ago by Shettland
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• Add skip asciigenome by default to viralrecon template

  #327 opened 4 months ago by saramonzon
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• Viralrecon creates mapping_illumina.xlsx with columns that are not always necessary

  #328 opened 4 months ago by victor5lm
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• Version update of workflows in the mag template

  #329 opened 4 months ago by Daniel-VM
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• Lablog_viralrecon does not download ncbi references when they do not belong to any family

  #309 opened 4 months ago by jaimeozaez
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• viralrecon template remove sorted.bams only for amplicons, not for metagenomic

  #311 opened 4 months ago by svarona
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• Several improvements for lablog_viralrecon

  #303 opened 5 months ago by jaimeozaez
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• Bioinfo-doc does not apply new-lines when creating the e-main notes

  #289 opened 5 months ago by svarona
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• Non-interactive mode for lablog_viralrecon running

  #302 opened 5 months ago by jaimeozaez
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• Update to nf-core/bacass v2.3.0 and Adjust Paths

  #283 opened 5 months ago by Daniel-VM
  1

• Wrong date grep in mtbseq lablog

  #297 opened 5 months ago by Shettland
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• Viralrecon's lablog fails at creating new lablog files when new references are downloaded

  #298 opened 5 months ago by victor5lm
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• Include AMRFinderPlus in Characterization template

  #286 opened 6 months ago by Shettland
  1

• Create a script for getting stats from outbreak services

  #292 opened 6 months ago by jaimeozaez
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• amrfinderplus implementation with singularity instead of conda

  #291 opened 6 months ago by Shettland
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• Add a check stage before setting "in progress" services when new-service is executed

  #285 opened 6 months ago by jaimeozaez
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• Include Multiqc_report.html in RESULTS folder for every service

  #252 opened 6 months ago by Shettland
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• Add nextflow pipeline's multiQC reports to RESULTS delivered

  #245 opened 6 months ago by svarona
  1

• wkhtmltopdf error in bioinfo-doc

  #243 opened 7 months ago by Shettland
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• Remove absolute path for wkhtmltopdf executable

  #275 opened 7 months ago by saramonzon
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• Implement --dev flag to prevent email notifications during testing phases

  #262 opened 7 months ago by Daniel-VM
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• Update SFTP copy files

  #235 opened 7 months ago by svarona
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• Check path where nexflow downloads the needed singularity images

  #269 opened 7 months ago by jaimeozaez
  1

• Create results lablog for exometrio template and update picard-results filename

  #234 opened 7 months ago by Shettland
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• All lablogs should include lablog in its name

  #236 opened 8 months ago by svarona
  1

• Complete documentation for mRNAseq

  #246 opened 8 months ago by Daniel-VM
  0