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Changes for v1.1.1#170

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abhi18av merged 65 commits intomasterTORCH-Consortium/MAGMA:masterfrom developTORCH-Consortium/MAGMA:developCopy head branch name to clipboardSep 9, 2023

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Commits

Commits on Aug 10, 2023

• Update default_params.config

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  LennertVerboven

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• Create variant_table_to_fasta.py

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  LennertVerboven

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• Update default_params.config

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  TimHHH

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Commits on Aug 12, 2023

• Added the resistance database for TBProfiler version 5

  LennertVerboven

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• Update magma-env-1.yml

  LennertVerboven

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• Update setup_conda_envs.sh

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Commits on Aug 13, 2023

• Update default_params.config

  LennertVerboven

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• Update build.sh

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• Update Dockerfile

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• Update summarize_resistance.py

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  LennertVerboven

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• replace sed -> python scripts [ci skip]

  abhi18av

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• tweak for python2 [ci skip]

  abhi18av

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• document the different GVCF files

  abhi18av

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• fix typo [ci skip]

  abhi18av

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Commits on Aug 16, 2023

• Added the structural variant workflow and the resistance profiling of these variants.

  LennertVerboven

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• Merge branch 'update_tbprofiler_v5' of https://github.com/TORCH-Consortium/MAGMA into update_tbprofiler_v5

  LennertVerboven

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• cleanup

  LennertVerboven

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• Update setup_conda_envs.sh

  LennertVerboven

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• Update default_params.config

  LennertVerboven

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• Update rename_vcf_chrom.py

  LennertVerboven

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• Update rename_vcf_chrom.py

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Commits on Aug 17, 2023

• interim commit [ci skip]

  abhi18av

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• tweak variants to fasta [ci skip]

  abhi18av

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• accommodate the new design for structural variants [ci skip]

  abhi18av

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• fix imports [ci skip]

  abhi18av

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• fix input to workflow [ci skip]

  abhi18av

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• dev [ci skip]

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• dev [ci skip]

  abhi18av

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• build and push new containers for v1.1.1 [ci skip]

  abhi18av

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• Fixed the summarize resistance script and added the strcutural variants to it

  LennertVerboven

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• fixed some merge conflicts

  LennertVerboven

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• Merge pull request #168 from TORCH-Consortium/replace_sed

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  LennertVerboven

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• add back the bc dependency [ci skip]

  abhi18av

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• Update magma-env-1.yml

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  LennertVerboven

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• minimal change, add bc to container-2 only [ci skip]

  abhi18av

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• Update CHANGELOG.md

  LennertVerboven

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• Changed the permissions on some files

  LennertVerboven

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• Merge branch 'update_tbprofiler_v5' of https://github.com/TORCH-Consortium/MAGMA into update_tbprofiler_v5

  LennertVerboven

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• Fixed a typo in the script causing structural variants to not shoiw up

  LennertVerboven

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• Merge pull request #169 from TORCH-Consortium/update_tbprofiler_v5

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  LennertVerboven

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Commits on Aug 18, 2023

• add the default lineage reference files GVCF [ci skip]

  abhi18av

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• tweak comments [ci skip]

  abhi18av

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• tweak comments in the config file [ci skip]

  abhi18av

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Commits on Aug 20, 2023

• fixed the filtering bug

  LennertVerboven

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• finilize filtering bug fix

  LennertVerboven

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Commits on Aug 21, 2023

• Merge pull request #173 from TORCH-Consortium/filtering_bug

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  LennertVerboven

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Commits on Aug 24, 2023

• added sample filtering for the structural variant workflow

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Commits on Aug 26, 2023

• Merge pull request #174 from TORCH-Consortium/sv_filtered

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  LennertVerboven

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• Update structural_variants_analysis_wf.nf

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Commits on Aug 27, 2023

• Moved the vcf filenames from bcftools merge into a file such that the command does not become impossibly long

  LennertVerboven

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Commits on Aug 28, 2023

• Added multithreading to tbprofiler

  LennertVerboven

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• Fixed it that the file listing samples actually contains the newlines

  LennertVerboven

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• removed sorting from merge channels

  LennertVerboven

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• Merge pull request #175 from TORCH-Consortium/fix_large_commands

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  vrennie

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Commits on Aug 31, 2023

• Fixed bug in the bcftools merge where the input file was uanavailble on AWS

  LennertVerboven

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Commits on Sep 4, 2023

• tweak the readme [ci skip]

  abhi18av

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• add params specific to iqtree [ci skip]

  abhi18av

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• Update iqtree.nf

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  TimHHH

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Commits on Sep 6, 2023

• switch the script to python3 [ci skip]

  abhi18av

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• add view for file filtering logic [ci skip]

  abhi18av

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• refactor the location of view [ci skip]

  abhi18av

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• refactor the location of view [ci skip]

  abhi18av

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• refactor the location of view [ci skip]

  abhi18av

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• revert to binary invocation of the script in SNPEFF [ci skip]

  abhi18av

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• use generic python [ci skip]

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