Commit b485fdf

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Merge pull request #7 from nourmahfel/dev

Update pipeline

2 parents 68c8b85 + f9a6622 commit b485fdfCopy full SHA for b485fdf

146 files changed

+4861

-7270

lines changed

.prettierignore
assets
- data/annotate_str
  - variant_catalog_hg38.json
- email_template.html
- samplesheet.csv
- samplesheet_test_fastq.csv
- samplesheet_test_ubam.csv
- schema_input.json
- test_data
  - HG002_ONT.fastq.gz
  - test.exclude.bed
bin
conf
fix_nf_format.py
modules.json
modules
- local
  - SvAnna
    - main.nf
  - annotate_str
    - main.nf
  - clair3_fixVCF
    - main.nf
  - downsample_sv
    - main.nf
  - exomiser
    - main.nf
  - hificnv
    - main.nf
  - methbat
    - main.nf
  - normalize_cutesv
    - main.nf
  - normalize_merged_sv
    - main.nf
  - round_dp
    - main.nf
  - spectre
    - main.nf
  - straglr
    - main.nf
  - survivor_vcftobed
    - main.nf
  - svim
    - main.nf
  - truvari/collapse
    - main.nf
  - unifyvcf_geneyx
    - main.nf
  - winnowmap
    - main.nf
- nf-core
  - ensemblvep
    - filtervep
    - vep
  - fastqc
  - hiphase
  - jasminesv
  - longphase/phase
    - main.nf
    - meta.yml
    - tests
      - main.nf.test.snap
  - modkit/pileup
    - environment.yml
    - main.nf
    - tests
      - main.nf.test.snap
  - multiqc
  - paraphase
  - pbsv/call
  - stranger
  - survivor
    - filter
    - merge
  - trgt/genotype
nextflow.config
nextflow_schema.json
subworkflows
- local
  - align.nf
  - assemble_reads.nf
  - bam2fastq.nf
  - call_cnv_spectre.nf
  - call_hificnv.nf
  - call_snv.nf
  - call_str.nf
  - call_sv.nf
  - consensuSV.nf
  - filter_sv.nf
  - longphase.nf
  - merge_snv.nf
  - merge_sv.nf
  - methyl.nf
  - methylation.nf
  - mosdepth.nf
  - nanoplot.nf
  - str.nf
  - sv.nf
  - unify_vcf.nf
  - utils_nfcore_longraredisease_pipeline
    - main.nf
- nf-core
  - utils_nextflow_pipeline
    - main.nf
  - utils_nfcore_pipeline
    - main.nf
  - utils_nfschema_plugin
    - main.nf
    - tests
tests
- bam2fastq.nf.test
- main.nf.test
workflows
- longraredisease.nf

146 files changed

+4861

-7270

lines changed

`‎.prettierignore‎`

-Original file line number
+Diff line change
 *.pyc
 bin/
 ro-crate-metadata.json
 -node_modules/
 -dist/
 -build/

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