TORCH-Consortium MAGMA issues

TORCH-Consortium / MAGMA

A pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research

https://doi.org/10.1371/journal.pcbi.1011648

GNU General Public License v3.0

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issues

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Update bwa_k66.config

#226 abhi18av closed 1 month ago
0
new config file not working

#225 vrennie closed 2 months ago
1
add a license header for all source files

#224 abhi18av closed 1 month ago
0
adding sandbox_vm config for user testing

#223 vrennie closed 2 months ago
0
Next release v2.1.0

#222 abhi18av opened 2 months ago
0
Implementation of multiqc report generation for the V1 report

#221 Mxrcon opened 3 months ago
3
Add a test profile in the pipeline

#220 abhi18av closed 3 months ago
1
Accommodate Mbovis reference

#219 abhi18av opened 3 months ago
0
Implement a test profile in the pipeline for new users

#217 abhi18av closed 2 months ago
0
Pipeline failing with older fastq file

#216 RuanSpies21 opened 3 months ago
20
Update convert_ismapper_to_vcf.py

#215 vrennie closed 4 weeks ago
31
Update convert_ismapper_to_vcf.py

#214 vrennie closed 4 months ago
6
Add clarification for bqsr recaliberated files

#213 abhi18av closed 4 months ago
0
Process `UTILS_MERGE_COHORT_STATS (joint_name: joint)` terminated with an error exit status (1)

#211 MohdKhairulNizam closed 4 months ago
3
Refactor containers v200

#210 abhi18av closed 4 months ago
1
Structural variants v2 - accommodate transposable elements

#209 abhi18av closed 4 months ago
3
[BUG FIX] Related to issue #207 on conda_local profile

#208 Mxrcon opened 4 months ago
1
MINOR_VARIANTS_ANALYSIS_WF:TBPROFILER_VCF_PROFILE__LOFREQ error on conda config

#207 Mxrcon opened 4 months ago
1
Iteration for 2.0.0-beta release

#206 abhi18av closed 3 months ago
0
Compute FASTQ stats from the input samplesheet

#205 abhi18av closed 4 months ago
0
Simplify the samplesheet

#204 abhi18av closed 4 months ago
1
Remove the custom built who-magma database for tb-profiler

#203 abhi18av closed 5 months ago
0
Improve strand bias filter for minor/infrequent variants

#202 abhi18av closed 5 months ago
2
Iteration for v2.0.0-beta release - update GVCF

#201 abhi18av closed 5 months ago
0
Add MTB_L10 reference in the bundled GVCF

#200 abhi18av closed 5 months ago
1
Rethink FASTQ validation and accommodate FusionFS

#199 abhi18av closed 5 months ago
0
Tweaks to make the pipeline compatible with fusionfs

#198 abhi18av closed 5 months ago
0
Enable the ITOL annotations in the tb-profiler command

#197 abhi18av closed 4 months ago
1
Changed the case of the probaiblities

#196 LennertVerboven closed 5 months ago
0
Patch the multiple infection filtering logic

#195 abhi18av closed 6 months ago
1
Update NC-000962-3-H37Rv.dict

#194 vrennie closed 6 months ago
1
Add resistance summary for multiple-infections

#192 abhi18av closed 6 months ago
0
Release v2.0.0 with updated TBprofiler and new NTMprofiler results

#191 abhi18av closed 5 months ago
2
Add NTM profiler and separate the profiler containers

#190 abhi18av closed 7 months ago
1
Improve the structure of results directory

#189 abhi18av closed 8 months ago
6
Transition to nf-core standard for pipeline and documentation

#188 abhi18av opened 8 months ago
0
Magma via Conda Env

#186 foamy1881 closed 8 months ago
1
WHO database v2 and TB-profiler v6.x

#185 mdediegofuertes closed 7 months ago
8
Add a config file for the low memory users

#184 vrennie closed 10 months ago
3
Running on a computer with low memory

#182 vrennie closed 1 year ago
0
Adding a low memory option

#181 vrennie closed 11 months ago
0
Pipeline bug (MINOR_VARIANTS_ANALYSIS_WF:TBPROFILER_VCF_PROFILE__LOFREQ)

#180 vrennie closed 11 months ago
9
Docs update

#178 abhi18av closed 1 year ago
0
Resistance DB updates for a new minor release (with new containers)

#177 abhi18av closed 7 months ago
8
Final pre-release documentation tweaks

#176 abhi18av closed 1 year ago
0
Fix large commands

#175 LennertVerboven closed 1 year ago
0
added sample filtering for the structural variant workflow

#174 LennertVerboven closed 1 year ago
0
Filtering bug

#173 LennertVerboven closed 1 year ago
1
Filtering bug

#172 LennertVerboven closed 1 year ago
0
Structural variants workflow only on samples that passed QC

#171 LennertVerboven closed 1 year ago
1