TORCH-Consortium/MAGMA

Issues

• new config file not working

  #225 opened 2 months ago by vrennie
  1

• Pipeline failing with older fastq file

  #216 opened 3 months ago by RuanSpies21
  20

• Implement a test profile in the pipeline for new users

  #217 opened 2 months ago by abhi18av
  0

• Publish a condensed MultiQC report with the relevant statistics

  #99 opened 3 years ago by abhi18av
  7

• Thread for possible enhancements in future

  #120 opened 2 years ago by abhi18av
  16

• MINOR_VARIANTS_ANALYSIS_WF:TBPROFILER_VCF_PROFILE__LOFREQ error on conda config

  #207 opened 4 months ago by Mxrcon
  1

• Coordinates for Structural Varinats in DR (post-release small issues)

  #93 opened 3 years ago by TimHHH
  5

• Process `UTILS_MERGE_COHORT_STATS (joint_name: joint)` terminated with an error exit status (1)

  #211 opened 4 months ago by MohdKhairulNizam
  3

• Speeding up minor variants analysis

  #165 opened a year ago by vrennie
  2

• Consider adding a separate container for processes which are expected to change (e.g. tb-profiler)

  #167 opened 5 months ago by abhi18av
  1

• Enhance the cohort based drug resistance summary per gene or drug

  #149 opened 5 months ago by abhi18av
  1

• Standardisation of MGIT-sputum-culture pairs

  #166 opened a year ago by vrennie
  1

• Implement pipeline execution checkpoints

  #148 opened 5 months ago by abhi18av
  3

• Add/improve default configs for common infra

  #125 opened 5 months ago by abhi18av
  1

• Transition to nf-core standard for pipeline and documentation

  #188 opened 8 months ago by abhi18av
  0

• Magma via Conda Env

  #186 opened 8 months ago by foamy1881
  1

• Pipeline bug (MINOR_VARIANTS_ANALYSIS_WF:TBPROFILER_VCF_PROFILE__LOFREQ)

  #180 opened a year ago by vrennie
  9

• Running on a computer with low memory

  #182 opened a year ago by vrennie
  0

• Structural variants workflow only on samples that passed QC

  #171 opened a year ago by LennertVerboven
  1

• Bundle lineage-references and outgroup

  #162 opened a year ago by abhi18av
  2

• Memory requirements

  #138 opened a year ago by TORCH-UAntwerpen
  3

• list highest relabundance strain when threshold is not met

  #101 opened a year ago by TORCH-UAntwerpen
  1

• Supply EXIT-RIF expansion set

  #127 opened a year ago by TimHHH
  6

• Refactor pipeline to move away from use of sed (failure during phylogeny snp-sites step)

  #163 opened a year ago by abhi18av
  7

• Update to TBProfiler database

  #159 opened 2 years ago by LennertVerboven
  1

• Cleanup output directories

  #151 opened 2 years ago by TimHHH
  4

• Add another round of TBProfiler for detection of structural variants

  #146 opened 2 years ago by vrennie
  3

• Add info about the sequencing tech TAG and reflect that on the reports

  #150 opened 2 years ago by abhi18av
  7

• Iterative creation/use of cohort gvcf files

  #157 opened 2 years ago by vrennie
  4

• "Sample has not enough data to estimate library parameters!"

  #155 opened 2 years ago by jloubser
  1

• Remove old fastq.STATUS.tsv files

  #144 opened 2 years ago by LennertVerboven
  0

• Make use of labels to simplify resource specification

  #77 opened 2 years ago by abhi18av
  2

• Rename the pipeline to magma

  #130 opened 2 years ago by abhi18av
  0

• Retry the GATK_VARIANT_RECALIBRATOR with reduced gaussians on failure

  #73 opened 3 years ago by abhi18av
  2

• Proposal for replacing QuantTB with TBprofiler

  #129 opened 2 years ago by TimHHH
  2

• Refactor the usage of tbprofiler vcf_profile

  #104 opened 2 years ago by TimHHH
  7

• [Input samplesheet validation] Sample names with point can result in accidental sample merge

  #102 opened 2 years ago by TimHHH
  5

• Add FastQ file checkpoint

  #131 opened 2 years ago by vrennie
  1

• setup_conda_envs.sh odd rm command

  #133 opened 2 years ago by TimHHH
  1

• Failing samples on QUANT_TB should also be captured in the stats

  #106 opened 2 years ago by abhi18av
  5

• Exclusion of DR markers phylogeny

  #115 opened 2 years ago by TimHHH
  2

• Explore custom log and warning messages (post-release)

  #96 opened 3 years ago by abhi18av
  1

• Implement check for fastq integrity.

  #90 opened 3 years ago by TimHHH
  5

• Consider providing a GVCF file for EXIT-RIF dataset

  #74 opened 3 years ago by abhi18av
  9

• Results large run EXIT-RIF

  #80 opened 3 years ago by TimHHH
  7

• Update readme to redirect users to the website

  #83 opened 3 years ago by abhi18av
  0

• Simplify the version of softwares via a single conda.yml env file

  #87 opened 3 years ago by abhi18av
  0

• Add a MULTIPLE_INFECTION_THRESHOLD_MET field in quanttb report

  #88 opened 3 years ago by abhi18av
  2

• Update the quanttb report to accommodate refname

  #89 opened 3 years ago by abhi18av
  1

• Problems with tb-profiler WHO database

  #84 opened 3 years ago by abhi18av
  2