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Setup emergennce new variant -- figure 6 in VILOCA manuscript (#4)
* viloca version + insert file * add collect co-occ muts * collect the samples that are ready * correct script name and output name * update bed file to only process necessary amplicons to distinguish BA.2 and BA.5 * reduce amount of samples to only cover the once including June * add test sample set * --keep-incomplete * rerun-incomplete false * --rerun-triggers mtime * update test sample * update * remove samples from sept from the analysis * samples that have high prio to be processed * increase viloca resource * exclude sample since: error of no reads found in requested region * skip merging because we loose too many reads * add envp mode * reduce mutation of interest where noting is happening in the data * process all samples from april and may -- exclude june for now * update viloca params * exclude samples end of may * new version of viloca * exclude samples with super low coverage * get coverage information of all samples * update output * update output * update output * typo * fix col of result dataframe * include june samples * updated notebook, 0 freq in white and no data in gray * update notebook with the final figure for the manuscript * update sample list and clean up * [add] readme with description of recreating figure * [add] readme with description of recreating figure * remove space
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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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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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240,C2_10_2022_12_10,20221223_HMLV2DRX2 | ||
241,C2_10_2022_12_17,20230105_HMLN2DRX2 | ||
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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