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| @@ -1,4 +1,4 @@ | ||
| fname_reference: resources/NC_045512.2.fasta | ||
| fname_insert_bed: resources/SARS-CoV-2.v532.insert.bed | ||
| fname_insert_bed: resources/SARS-CoV-2.v4.insert.bed | ||
| fname_samples: config/samples.csv | ||
| dir_path_samples: # add path to samples here |
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| This is a workflow that uses the parent workflow to process a specific set of samples to compute their divesity. | ||
| This workflow produces Figure 6 in the Manuscript of VILOCA. | ||
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| To reproduce the results and figure: | ||
| 1.) Clone the repository. | ||
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| 2.) Move into this directory: `cd resources/setup_emergence_new_variant` | ||
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| 3.) Install conda enviroments needed for the the workflow:`snakemake --conda-create-envs-only --use-conda -c1 --rerun-incomplete` | ||
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| 4.) Execute workflow. On slurm cluster the script `run_workflow.sh` can be used. | ||
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| 5.) When you received the two needed output files `results/all_cooccurring_mutations.csv` and `results/samples.all_coverage.csv`, figure can be generated with the notebook `workflow/notebooks/rise_of_ba.5.ipynb` |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| fname_reference: ../NC_045512.2.fasta | ||
| fname_insert_bed: ../SARS-CoV-2.insert.bed | ||
| fname_insert_bed: resources/SARS-CoV-2.insert.reduced.250bp.bed | ||
| fname_samples: config/samples.csv | ||
| dir_path_samples: /cluster/project/pangolin/work-vp-test/results/ |
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resources/setup_emergence_new_variant/config/samples.csv
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| ,sample,batch | ||
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| 242,C2_10_2022_12_24,20230105_HMLN2DRX2 | ||
| 243,D2_10_2022_12_04,20221216_HM2HNDRX2 | ||
| 244,D2_10_2022_12_11,20221223_HMLV2DRX2 | ||
| 245,D2_10_2022_12_18,20230105_HMLN2DRX2 | ||
| 246,D2_10_2022_12_25,20230105_HMLN2DRX2 | ||
| 247,E2_10_2022_12_05,20221216_HM2HNDRX2 | ||
| 248,E2_10_2022_12_12,20221223_HMLV2DRX2 | ||
| 249,E2_10_2022_12_19,20230105_HMLN2DRX2 | ||
| 250,E2_10_2022_12_26,20230105_HMLN2DRX2 | ||
| 251,F2_10_2022_12_06,20221216_HM2HNDRX2 | ||
| 252,F2_10_2022_12_13,20221223_HMLV2DRX2 | ||
| 253,F2_10_2022_12_20,20230105_HMLN2DRX2 | ||
| 254,F2_10_2022_12_27,20230105_HMLN2DRX2 | ||
| 255,H1_10_2022_12_07,20221223_HMLV2DRX2 | ||
| 256,H1_10_2022_12_14,20230105_HMLN2DRX2 | ||
| 257,H1_10_2022_12_21,20230105_HMLN2DRX2 |
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