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chore: move config accesses in wrappers to params #536

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chore: move config accesses in wrappers to params #536

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@tedil tedil commented Aug 2, 2024

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tedil added 30 commits August 2, 2024 16:07
@tedil
chore: alfred/qc: move config access to params
56db085
@tedil
chore: remove alfred/qc_external wrapper (unused)
d0c8d2c
@tedil
chore: arriba/run: move config access to params
bd25fab
@tedil
chore: arriba/run: move config access to params (pt 2)
d55a86b
@tedil
chore: ascat/*: move config access to params
affc68b
@tedil
chore: baf_file_generation: move config access to params
59d5f32
@tedil
chore: bbduk: move config access to params (might need str conversions)
ed6e0ca
@tedil
chore: {bcftools,platypus}/call_joint: move config access to params
f9fe113
@tedil
chore: bcftools/filter: rename params to args for consistency
260cdd2
@tedil
chore: bcftools/gvcf_to_vcf: move config access to params
9d40314
@tedil
chore: bcftools/heterozygous_variants: move config access to params
d0a4163
@tedil
chore: bcftools/merge_snv_vcf: move config access to params
5ad8316
@tedil
chore: bcftools/merge_vcf: move config access to params
6c11e19
@tedil
chore: bcftools/pileups: move config access to params
842225f
@tedil
chore: bcftools/protected: use snakemake type hints
6bcbcf3
@tedil
chore: bcftools/regions: use snakemake type hints
5aea5fd
@tedil
chore: bcftools/stats: remove unused wrapper
5040037
@tedil
chore: bcftools/TMB: move config access to params
a3d5ec7
@tedil
chore: bcftools_call: move config access to params
1c6b52f
@tedil
chore: bcftools_roh: move config access to params
c4fca92
@tedil
chore: only import snakemake.script when type checking
1d79c9b
@tedil
fix: alfred/qc incorrect param name
f8c9c9e
@tedil
chore: bed_jaccard_operations: import snakemake.script.snakemake for …
1c136b9 
…type hints
@tedil
chore: bed_venn: import snakemake.script.snakemake for type hints
a33de05
@tedil
chore: bwa: move config access to params
dac4295
@tedil
chore: bwa_mem2: move config access to params
31821ae
@tedil
chore: canvas/somatic_wgs: move config access to params
aad0e80
@tedil
chore: cbioportal/case_lists: move config access to params
6b7994a
@tedil
chore: cbioportal/clinical_data: move config access to params
c5b1430
@tedil
add FIXME for cbioportal/clinical_data wrapper+model combo
a086273
@tedil tedil linked an issue Aug 22, 2024 that may be closed by this pull request
Wrappers: Move config accesses to params #513
Open
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Wrappers: Move config accesses to params
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@tedil