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Changes for v1.1.1 #170

Merged
merged 65 commits into from
Sep 9, 2023
Merged

Changes for v1.1.1 #170

merged 65 commits into from
Sep 9, 2023

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abhi18av
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@abhi18av abhi18av commented Aug 18, 2023 •
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This PR adds support for

  • Structural variants analysis
  • Replaces the sed scripts with python for reproducibility when using pure Conda setup
  • Updated containers with dependencies
  • Updated TB-profiler database
  • The new GVCF reference

LennertVerboven and others added 30 commits August 10, 2023 12:20
@LennertVerboven
Update default_params.config
46444a7 
Added the site_representation_cutoff
@LennertVerboven
Create variant_table_to_fasta.py
2df215a 
Added the script which replace the sed commands used to create the fasta file for phylogeny
@TimHHH
Update default_params.config
9f09556 
Moved site representation to EXPERIENCED USERS section
@LennertVerboven
Added the resistance database for TBProfiler version 5
7c871f7
@LennertVerboven
Update magma-env-1.yml
9735abd
@LennertVerboven
Update setup_conda_envs.sh
340a98f
@LennertVerboven
Update default_params.config
a943ad7
@LennertVerboven
Update build.sh
e2ba4c3
@LennertVerboven
Update Dockerfile
7e4d928
@LennertVerboven
Update summarize_resistance.py
8c7bf6c 
Added the command line argument for the structural variant results directory. They are not yet added to the summary file, as this requires testing with real data.
@abhi18av
replace sed -> python scripts [ci skip]
e590d85
@abhi18av
tweak for python2 [ci skip]
8a0288f
@abhi18av
document the different GVCF files
25f343e
@abhi18av
fix typo [ci skip]
2e9d1d0
@LennertVerboven
Added the structural variant workflow and the resistance profiling of…
fe42e9c 
… these variants.
@LennertVerboven
Merge branch 'update_tbprofiler_v5' of https://github.com/TORCH-Conso…
9f2a7ec 
…rtium/MAGMA into update_tbprofiler_v5
@LennertVerboven
cleanup
79dfc4a
@LennertVerboven
Update setup_conda_envs.sh
dbbad0d
@LennertVerboven
Update default_params.config
7c35e55
@LennertVerboven
Update rename_vcf_chrom.py
33f8be5
@LennertVerboven
Update rename_vcf_chrom.py
c6e4704
@abhi18av
interim commit [ci skip]
4e7d69f
@abhi18av
tweak variants to fasta [ci skip]
8e3e1f3
@abhi18av
accommodate the new design for structural variants [ci skip]
80e9273
@abhi18av
fix imports [ci skip]
4e2995c
@abhi18av
fix input to workflow [ci skip]
0d5f1dc
@abhi18av
dev [ci skip]
294243f
@abhi18av
dev [ci skip]
f349e50
@abhi18av
build and push new containers for v1.1.1 [ci skip]
d43b341
@LennertVerboven
Fixed the summarize resistance script and added the strcutural varian…
6427271 
…ts to it
abhi18av and others added 12 commits August 18, 2023 06:29
@abhi18av
tweak comments in the config file [ci skip]
b218fb6
@LennertVerboven
fixed the filtering bug
fe82c3d
@LennertVerboven
finilize filtering bug fix
c2af534
@LennertVerboven
Merge pull request #173 from TORCH-Consortium/filtering_bug
e0a4a45 
Filtering bug
@LennertVerboven
added sample filtering for the structural variant workflow
88a152b
@LennertVerboven
Merge pull request #174 from TORCH-Consortium/sv_filtered
28991fa 
added sample filtering for the structural variant workflow
@LennertVerboven
Update structural_variants_analysis_wf.nf
5bc0b87
@LennertVerboven
Moved the vcf filenames from bcftools merge into a file such that the…
c3e125c 
… command does not become impossibly long
@LennertVerboven
Added multithreading to tbprofiler
4190a3a
@LennertVerboven
Fixed it that the file listing samples actually contains the newlines
a23a4a9
@LennertVerboven
removed sorting from merge channels
4bf84a0
@vrennie
Merge pull request #175 from TORCH-Consortium/fix_large_commands
3aba60a 
Fix large commands
@LennertVerboven LennertVerboven marked this pull request as ready for review August 30, 2023 07:10
@abhi18av abhi18av linked an issue Sep 8, 2023 that may be closed by this pull request
Structural variants workflow only on samples that passed QC #171
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@LennertVerboven
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Looks good to me

@abhi18av abhi18av merged commit c84ee9e into master Sep 9, 2023
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@LennertVerboven LennertVerboven LennertVerboven approved these changes

@vrennie vrennie Awaiting requested review from vrennie

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@abhi18av @LennertVerboven @TimHHH @vrennie