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Setup emergennce new variant -- figure 6 in VILOCA manuscript (#4)
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* 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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LaraFuhrmann authored Apr 8, 2024
1 parent 2a03a51 commit 79bb431
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Showing 16 changed files with 1,193 additions and 212 deletions.
2 changes: 1 addition & 1 deletion config/config.yaml
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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
13 changes: 12 additions & 1 deletion resources/setup_emergence_new_variant/README.md
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@@ -1 +1,12 @@
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.

To reproduce the results and figure:
1.) Clone the repository.

2.) Move into this directory: `cd resources/setup_emergence_new_variant`

3.) Install conda enviroments needed for the the workflow:`snakemake --conda-create-envs-only --use-conda -c1 --rerun-incomplete`

4.) Execute workflow. On slurm cluster the script `run_workflow.sh` can be used.

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`
2 changes: 1 addition & 1 deletion resources/setup_emergence_new_variant/config/config.yaml
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@@ -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/
199 changes: 0 additions & 199 deletions resources/setup_emergence_new_variant/config/samples.csv
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184,C2_10_2022_10_08,20221021_HJ3NNDRX2
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240,C2_10_2022_12_10,20221223_HMLV2DRX2
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242,C2_10_2022_12_24,20230105_HMLN2DRX2
243,D2_10_2022_12_04,20221216_HM2HNDRX2
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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
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256,H1_10_2022_12_14,20230105_HMLN2DRX2
257,H1_10_2022_12_21,20230105_HMLN2DRX2
Original file line number Diff line number Diff line change
Expand Up @@ -14,14 +14,14 @@ default-resources:
# - qos=<name-of-quality-of-service>
- mem_mb=2000
- runtime=15
restart-times: 3
restart-times: 1
max-jobs-per-second: 10
max-status-checks-per-second: 1
local-cores: 1
latency-wait: 60
jobs: 500
keep-going: True
rerun-incomplete: True
rerun-incomplete: False
printshellcmds: True
scheduler: greedy
use-conda: True
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