From 7729df52fce9b87ab5e4e6941ab4552642e4015d Mon Sep 17 00:00:00 2001
From: Johannes Gawron <Johannes.Gawron@bsse.ethz.ch>
Date: Wed, 26 Jun 2024 17:00:14 +0200
Subject: [PATCH] adapted output format

---
 .pre-commit-config.yaml                     | 2 --
 experiments/config/config.yaml              | 4 ++--
 experiments/workflow/Snakefile              | 4 +++-
 experiments/workflow/resources/template.Rmd | 3 ++-
 experiments/workflow/rules/base.smk         | 4 ++--
 5 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1275aa8..9cf9fd5 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,9 +7,7 @@ repos:
     rev: v0.4.2
     hooks:
       - id: style-files
-        args: [--warn_only]
       - id: parsable-R  
-        args: [--warn-only]
       - id: lintr
         args: [--warn_only]
         verbose: true  
diff --git a/experiments/config/config.yaml b/experiments/config/config.yaml
index c2eadf3..137cc67 100644
--- a/experiments/config/config.yaml
+++ b/experiments/config/config.yaml
@@ -1,5 +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']
+sample: ['Br11']
+#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/workflow/Snakefile b/experiments/workflow/Snakefile
index bd5dcbe..cbde19e 100644
--- a/experiments/workflow/Snakefile
+++ b/experiments/workflow/Snakefile
@@ -22,7 +22,9 @@ include: "rules/base.smk"
 
 all_files = []
 for sample in SAMPLES:
-    all_files.append((PROJECT_DIR / "data" / "htmls" / f"{sample}.html").resolve())
+    all_files.append(
+        (PROJECT_DIR / "data" / "htmls" / f"{sample}_treeSampling.html").resolve()
+    )
     all_files.append(
         (PROJECT_DIR / "data" / "htmls" / f"{sample}_topSeparators.html").resolve()
     )
diff --git a/experiments/workflow/resources/template.Rmd b/experiments/workflow/resources/template.Rmd
index 18abb2a..8376d43 100644
--- a/experiments/workflow/resources/template.Rmd
+++ b/experiments/workflow/resources/template.Rmd
@@ -32,6 +32,7 @@ simulationInputFolder <- params$simulationInputFolder
 treeName <- params$treeName
 nTreeSamplingEvents <- params$nSamplingEvents
 nMutationSamplingEvents <- params$nSamplingEvents
+nSamplingEvents <- params$nSamplingEvents
 ```
 
 ## Loading data
@@ -155,7 +156,7 @@ for (clusterSize in 2:5) {
         nOligoclonalClusters2 <- nOligoclonalClusters2 + 1
         oligoclonal <- TRUE
       }
-      splittingSummary2 <- rbind(splittingSummary2, data.frame(Color = color, Oligoclonal = oligoclonal, ClusterSize = clusterSize))
+      splittingSummary2 <- rbind(splittingSummary2, data.frame(Color = color, Oligoclonal = oligoclonal, ClusterSize = clusterSize, cutoff = cutoffsBranchingProbabilities[(cutoffsBranchingProbabilities$clusterSize == clusterSize), 2], mean_splitting_score = branchingProbs))
     }
   })
 }
diff --git a/experiments/workflow/rules/base.smk b/experiments/workflow/rules/base.smk
index 3e94dc0..cdcb8c2 100644
--- a/experiments/workflow/rules/base.smk
+++ b/experiments/workflow/rules/base.smk
@@ -79,7 +79,7 @@ rule render_markdown_file:
         input_dir=INPUT_FOLDER,
         simulation_dir=SIMULATION_FOLDER,
     resources:
-        mem_mb=2048,
+        mem_mb_per_cpu=4096,
         runtime=2880,
     threads: 16
     conda:
@@ -88,7 +88,7 @@ rule render_markdown_file:
         PROJECT_DIR / "logs" / "render_markdown_file.{SAMPLE}.log",
     shell:
         """
-        ( Rscript -e "rmarkdown::render('{input}', output_file = '{output}')", params = list(inputFolder = {params.input_dir}, nSamplingEvents = {params.sampling_depth}, simulationInputFolder = {params.simulation_dir}, treeName = {wildcard.SAMPLE}, functionsScript = {params.script_dir}) ) &> {log}
+        ( Rscript -e "rmarkdown::render('{input}', output_file = '{output}', params = list(inputFolder = '{params.input_dir}', nSamplingEvents={params.sampling_depth}, simulationInputFolder = '{params.simulation_dir}', treeName = '{wildcards.SAMPLE}', functionsScript = '{params.script_dir}'))" ) &> {log}
         """