adapted input specification in config

cbg-ethz · Jun 7, 2024 · 4713c82 · 4713c82
1 parent 0ce2ee8
commit 4713c82
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Showing 5 changed files with 274 additions and 151 deletions.
diff --git a/experiments/config/config.yaml b/experiments/config/config.yaml
@@ -1,3 +1,5 @@
 #sample: ['Lu2']
 sample: ['Br11', 'Br7', 'Br61', 'Br38', 'LM2', 'Pr9', 'Br23','Br39', 'Br57', 'Lu2', 'Br16_AC', 'Br16_B', 'Br16_C', 'Br26', 'Br44', 'Lu7', 'Br30', 'Br45', 'Ov8', 'Br37', 'Br46', 'Brx50', 'Pr6']
 author: Johannes Gawron
+input: /cluster/work/bewi/members/jgawron/projects/CTC/input_folder
+simulations: /cluster/work/bewi/members/jgawron/projects/CTC/simulations/simulations2
diff --git a/experiments/data/htmls/Br38.html b/experiments/data/htmls/Br38.html
diff --git a/experiments/workflow/Snakefile b/experiments/workflow/Snakefile
@@ -5,6 +5,10 @@ PROJECT_DIR = Path(workflow.basedir).parent
 SCRIPT_DIR = Path(workflow.basedir) / 'scripts'
 RESOURCES_DIR = Path(workflow.basedir) / 'resources'
 markdown_helper_functions = (RESOURCES_DIR / 'functions.R').resolve().as_posix().replace('/', '\\/')
+input_folder = Path(config['input']).resolve().as_posix().replace('/','\\/')
+simulations_folder = Path(config['simulations']).resolve().as_posix().replace('/','\\/')
+
+
 print(markdown_helper_functions)
 
 ######Rules######

diff --git a/experiments/workflow/resources/template.Rmd b/experiments/workflow/resources/template.Rmd
@@ -20,8 +20,8 @@ The analysis takes a list of trees sampled from its posterior distribution as in
 
 ## Configure the script
 ```{r config}
-inputFolder <- "/Users/jgawron/Documents/projects/CTC_backup/input_folder"
-simulationInputFolder <- "/Users/jgawron/Documents/projects/CTC_backup/simulations/simulations2"
+inputFolder <- "__input_dir__"
+simulationInputFolder <- "__sim_dir__"
 treeName <- "__tree__"
 nTreeSamplingEvents <- __nSamplingEvents__
 nMutationSamplingEvents <- __nSamplingEvents__

diff --git a/experiments/workflow/rules/base.smk b/experiments/workflow/rules/base.smk
@@ -9,7 +9,9 @@ rule prepare_markdown_file:
     params:
         sampling_depth = 1000,
         script_dir =  {markdown_helper_functions},
-        author = config['author']
+        author = config['author'],
+        input_dir = input_folder,
+        simulation_dir = simulations_folder,
     log:
         PROJECT_DIR / 'logs' / 'prepare_markdown_file.{SAMPLE}.log',
     shell:
@@ -19,6 +21,8 @@ rule prepare_markdown_file:
         -e "s/__date__/$(date +'%Y-%m-%d')/g" \
         -e "s/__functionsScript__/{params.script_dir}/g" \
         -e "s/__author__/{params.author}/g" \
+        -e "s/__input_dir__/{params.input_dir}/g" \
+        -e "s/__sim_dir__/{params.simulation_dir}/g" \
         {input} > {output} ) &> {log}
         """
 
@@ -27,7 +31,7 @@ rule render_markdown_file:
         PROJECT_DIR / 'data' / 'markdowns' / '{SAMPLE}.Rmd',
     output:
         PROJECT_DIR / 'data' / 'htmls' / '{SAMPLE}.html',
-    threads: 8
+    threads: 16
     conda:
         Path(workflow.basedir) / 'envs' / 'R.yml',
     log: