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TORCH-Consortium
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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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new config file not working
#225
vrennie
closed
1 week ago
1
add a license header for all source files
#224
abhi18av
closed
3 days ago
0
adding sandbox_vm config for user testing
#223
vrennie
closed
1 week ago
0
Next release v2.0.1
#222
abhi18av
opened
2 weeks ago
0
Implementation of multiqc report generation for the V1 report
#221
Mxrcon
opened
1 month ago
3
Add a test profile in the pipeline
#220
abhi18av
closed
1 month ago
1
Accommodate Mbovis reference
#219
abhi18av
opened
1 month ago
0
Implement a test profile in the pipeline for new users
#217
abhi18av
closed
2 weeks ago
0
Pipeline failing with older fastq file
#216
RuanSpies21
opened
1 month ago
20
Update convert_ismapper_to_vcf.py
#215
vrennie
opened
2 months ago
29
Update convert_ismapper_to_vcf.py
#214
vrennie
closed
2 months ago
6
Add clarification for bqsr recaliberated files
#213
abhi18av
closed
2 months ago
0
Process `UTILS_MERGE_COHORT_STATS (joint_name: joint)` terminated with an error exit status (1)
#211
MohdKhairulNizam
closed
2 months ago
3
Refactor containers v200
#210
abhi18av
closed
2 months ago
1
Structural variants v2 - accommodate transposable elements
#209
abhi18av
closed
2 months ago
3
[BUG FIX] Related to issue #207 on conda_local profile
#208
Mxrcon
opened
2 months ago
1
MINOR_VARIANTS_ANALYSIS_WF:TBPROFILER_VCF_PROFILE__LOFREQ error on conda config
#207
Mxrcon
opened
2 months ago
1
Iteration for 2.0.0-beta release
#206
abhi18av
closed
1 month ago
0
Compute FASTQ stats from the input samplesheet
#205
abhi18av
closed
2 months ago
0
Simplify the samplesheet
#204
abhi18av
closed
2 months ago
1
Remove the custom built who-magma database for tb-profiler
#203
abhi18av
closed
3 months ago
0
Improve strand bias filter for minor/infrequent variants
#202
abhi18av
closed
3 months ago
2
Iteration for v2.0.0-beta release - update GVCF
#201
abhi18av
closed
3 months ago
0
Add MTB_L10 reference in the bundled GVCF
#200
abhi18av
closed
3 months ago
1
Rethink FASTQ validation and accommodate FusionFS
#199
abhi18av
closed
3 months ago
0
Tweaks to make the pipeline compatible with fusionfs
#198
abhi18av
closed
3 months ago
0
Enable the ITOL annotations in the tb-profiler command
#197
abhi18av
closed
2 months ago
1
Changed the case of the probaiblities
#196
LennertVerboven
closed
3 months ago
0
Patch the multiple infection filtering logic
#195
abhi18av
closed
4 months ago
1
Update NC-000962-3-H37Rv.dict
#194
vrennie
closed
4 months ago
1
Add resistance summary for multiple-infections
#192
abhi18av
closed
4 months ago
0
Release v2.0.0 with updated TBprofiler and new NTMprofiler results
#191
abhi18av
closed
3 months ago
2
Add NTM profiler and separate the profiler containers
#190
abhi18av
closed
5 months ago
1
Improve the structure of results directory
#189
abhi18av
closed
6 months ago
6
Transition to nf-core standard for pipeline and documentation
#188
abhi18av
opened
6 months ago
0
Magma via Conda Env
#186
foamy1881
closed
6 months ago
1
WHO database v2 and TB-profiler v6.x
#185
mdediegofuertes
closed
5 months ago
8
Add a config file for the low memory users
#184
vrennie
closed
8 months ago
3
Running on a computer with low memory
#182
vrennie
closed
10 months ago
0
Adding a low memory option
#181
vrennie
closed
10 months ago
0
Pipeline bug (MINOR_VARIANTS_ANALYSIS_WF:TBPROFILER_VCF_PROFILE__LOFREQ)
#180
vrennie
closed
10 months ago
9
Docs update
#178
abhi18av
closed
11 months ago
0
Resistance DB updates for a new minor release (with new containers)
#177
abhi18av
closed
5 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
Changes for v1.1.1
#170
abhi18av
closed
1 year ago
1
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