Merge branch 'mwham_develop' into 'master' (9513d275) · Commits · igmmbioinformatics / trio-whole-exome · GitLab

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9513d275

Commit 9513d275 authored 2 years ago by mwham

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Merge branch 'mwham_develop' into 'master'

NextFlow variant calling

See merge request !4

parents cc1e90d2 6d91c6c2

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README.md 66 additions, 27 deletions

README.md
main.nf 47 additions, 0 deletions

main.nf
nextflow.config 30 additions, 0 deletions

nextflow.config
pipeline/inputs.nf 33 additions, 19 deletions

pipeline/inputs.nf
pipeline/main.nf 0 additions, 128 deletions

pipeline/main.nf
pipeline/validation.nf 41 additions, 17 deletions

pipeline/validation.nf
pipeline/var_calling.nf 335 additions, 0 deletions

pipeline/var_calling.nf
tests/assets/input_data/ped_files/giab_test_non_trios.ped 7 additions, 0 deletions

tests/assets/input_data/ped_files/giab_test_non_trios.ped
tests/assets/input_data/ped_files/giab_test_trios.ped 6 additions, 0 deletions

tests/assets/input_data/ped_files/giab_test_trios.ped
tests/assets/input_data/sample_sheets/batch_1.tsv 7 additions, 7 deletions

tests/assets/input_data/sample_sheets/batch_1.tsv
tests/assets/input_data/sample_sheets/batch_2_md5_errors.tsv 2 additions, 2 deletions

tests/assets/input_data/sample_sheets/batch_2_md5_errors.tsv
tests/assets/input_data/sample_sheets/giab_test_non_trios.tsv 8 additions, 0 deletions

...s/assets/input_data/sample_sheets/giab_test_non_trios.tsv
tests/assets/input_data/sample_sheets/giab_test_trios.tsv 7 additions, 0 deletions

tests/assets/input_data/sample_sheets/giab_test_trios.tsv
tests/run_giab_tests.sh 31 additions, 0 deletions

tests/run_giab_tests.sh
tests/run_tests.sh 1 addition, 2 deletions

tests/run_tests.sh
tests/scripts/nextflow_detached.sh 0 additions, 0 deletions

tests/scripts/nextflow_detached.sh

with 621 additions and 202 deletions

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