genomic-medicine-sweden/nallo

Issues

• Add `--deepvariant_model_type` to override `--preset`

  #215 opened 3 months ago by fellen31
  0

• Don't allow HiPhase with `--preset ONT_R10`

  #217 opened 3 months ago by fellen31
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• Don't allow TRGT with `--preset ONT_R10`

  #216 opened 3 months ago by fellen31
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• Remove `CONVERT_ONT_READ_NAMES`

  #214 opened 3 months ago by fellen31
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• FastQC for samples with multiple files not working as expected.

  #211 opened 3 months ago by fellen31
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• Raw read QC workflow

  #210 opened 3 months ago by fellen31
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• [User Story] Visualise methylation

  #166 opened 4 months ago by fellen31
  2

• Running with non-allowed --preset gives ambiguous error

  #208 opened 3 months ago by fellen31
  0

• Use phased variants for SV annotation

  #207 opened 3 months ago by fellen31
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• Use phased variants for SNV annotation

  #206 opened 3 months ago by fellen31
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• [User Story] Improve runtime

  #184 opened 3 months ago by fellen31
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• Move SNV concatenation from short_variant_calling to after annotation

  #203 opened 3 months ago by fellen31
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• Rename short_variant_calling

  #205 opened 3 months ago by fellen31
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• Replace TABIX with `--write-index` for bcftools modules in short_variant_calling

  #204 opened 3 months ago by fellen31
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• Use groupKey in short_variant_calling to remove bottleneck

  #202 opened 3 months ago by fellen31
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• Consistent output file naming compatible with Housekeeper

  #154 opened 4 months ago by fellen31
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• Refactor echtvar encode

  #201 opened 3 months ago by fellen31
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• Refactor phasing workflow

  #149 opened 4 months ago by fellen31
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• Deprecate --extra_gvcfs

  #200 opened 3 months ago by fellen31
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• Remove or replace pacbio/hificnv with nf-core module

  #199 opened 3 months ago by fellen31
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• [User Story] Assure pipeline compatibility with CG production

  #198 opened 3 months ago by fellen31
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• Add whatshap/stats to MultiQC report

  #197 opened 3 months ago by fellen31
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• Add mosdepth to MultiQC report

  #196 opened 3 months ago by fellen31
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• Add hifiasm to MultiQC report

  #195 opened 3 months ago by fellen31
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• Remove or replace hiphase with nf-core module

  #193 opened 3 months ago by fellen31
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• Remove or replace whatshap/phase with nf-core module

  #194 opened 3 months ago by fellen31
  0

• Add bcftools stats for SNVs to MultiQC report

  #191 opened 3 months ago by fellen31
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• Add bcftools stats for SVs to MultiQC report

  #192 opened 3 months ago by fellen31
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• Add BCFTools stats for SVs

  #190 opened 3 months ago by fellen31
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• Add BCFTools stats for SNVs

  #189 opened 3 months ago by fellen31
  0

• Implement nf-test for structural_variant_calling

  #188 opened 3 months ago by fellen31
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• Remove or replace dipcall with nf-core module

  #187 opened 3 months ago by fellen31
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• call_paralogs bgzip not working with multiple genes

  #182 opened 3 months ago by fellen31
  0

• Increase resources for samtools/merge

  #169 opened 3 months ago by fellen31
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• Running without somalier sites gives no error

  #174 opened 4 months ago by fellen31
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• haplotagged files are named .bam.bam

  #172 opened 4 months ago by fellen31
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• Skip paralogs not defined

  #168 opened 4 months ago by fellen31
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• Whatshap phase outputs .err files

  #171 opened 4 months ago by fellen31
  0

• Mosdepth without bed doesn't work

  #175 opened 4 months ago by fellen31
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• Phased methylation pileups are overwritten

  #170 opened 4 months ago by fellen31
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• Test data can't be phased

  #167 opened 4 months ago by fellen31
  1

• Remove or replace modkit/pileup with nf-core module

  #165 opened 4 months ago by fellen31
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• Add a pipelines_testdata_base_path

  #160 opened 4 months ago by fellen31
  1

• Use new ont-preset in minimap2

  #164 opened 4 months ago by fellen31
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• Remove or replace bcftools/fillfromfasta with nf-core module

  #161 opened 4 months ago by fellen31
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• Missing module versions

  #155 opened 4 months ago by fellen31
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• Move PED-file generation to process

  #158 opened 4 months ago by fellen31
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• Add hifiasm trio-binning to test profile

  #157 opened 4 months ago by fellen31
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• Remove TRGT "processed" directory

  #144 opened 4 months ago by fellen31
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• Replace HiPhase with longphase

  #147 opened 4 months ago by fellen31
  0