Doc updates, updating format of sample sheets. Adding nextflow.config. Adding...
Doc updates, updating format of sample sheets. Adding nextflow.config. Adding main.nf entrypoint, moving param declarations there. Making most input parameters their own Channels.
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- README.md 68 additions, 27 deletionsREADME.md
- main.nf 47 additions, 0 deletionsmain.nf
- nextflow.config 30 additions, 0 deletionsnextflow.config
- pipeline/inputs.nf 10 additions, 10 deletionspipeline/inputs.nf
- pipeline/var_calling.nf 64 additions, 30 deletionspipeline/var_calling.nf
- tests/assets/input_data/ped_files/giab_test_non_trios.ped 7 additions, 0 deletionstests/assets/input_data/ped_files/giab_test_non_trios.ped
- tests/assets/input_data/ped_files/giab_test_trios.ped 6 additions, 0 deletionstests/assets/input_data/ped_files/giab_test_trios.ped
- tests/assets/input_data/sample_sheets/batch_1.tsv 7 additions, 7 deletionstests/assets/input_data/sample_sheets/batch_1.tsv
- tests/assets/input_data/sample_sheets/batch_2_md5_errors.tsv 2 additions, 2 deletionstests/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 deletionstests/assets/input_data/sample_sheets/giab_test_trios.tsv
- tests/run_giab_tests.sh 31 additions, 0 deletionstests/run_giab_tests.sh
- tests/run_tests.sh 1 addition, 2 deletionstests/run_tests.sh
- tests/scripts/nextflow_detached.sh 0 additions, 0 deletionstests/scripts/nextflow_detached.sh
main.nf
0 → 100644
nextflow.config
0 → 100644
tests/run_giab_tests.sh
0 → 100755
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