remove deduping from fastp

flu-crew · Jul 10, 2024 · 609d68a · 609d68a
1 parent 5d6b450
commit 609d68a
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Showing 4 changed files with 11 additions and 3 deletions.
diff --git a/Scripts/findAAChanges.R b/Scripts/findAAChanges.R
@@ -52,6 +52,11 @@ if(length(metadata.file) == 0L) {
 #Set multithreading and memory usage
 threads = as.numeric(gsub("\"", "", config$THREADS))
 
+# output.directory = "/Volumes/Extreme_SSD/cattle-hpai-june/experiment-study/variant_analysis"
+# vcftable.path = paste0(output.directory, "/variant-table.csv")
+# reference.path = paste0("/Volumes/Extreme_SSD/cattle-hpai-june/experiment-study/Reference/reference.fa")
+# threads = 4
+# metadata.file = NULL
 
 #############################################
 #### Should not need to modify below here

diff --git a/Scripts/outputSummary.R b/Scripts/outputSummary.R
@@ -39,6 +39,11 @@ if(length(group.names) == 0L) {
   group.names <- NULL
 }
 
+# output.directory = "/Volumes/Extreme_SSD/cattle-hpai-june/experiment-study/variant_analysis"
+# aa.table.path = paste0("/Volumes/Extreme_SSD/cattle-hpai-june/experiment-study/curated_database.csv")
+# threads = 4
+# group.names = NULL
+
 #############################################
 #### Should not need to modify below here
 #############################################
@@ -191,7 +196,7 @@ for (i in 1:length(group.values)){
 }# i loop
 
 #Saves final data
-write.table(all.data, paste0(output.directory, "/animal_summary_curated_sites.txt"),
+write.table(all.data, paste0(output.directory, "/summary_curated_sites.txt"),
             row.names = F, quote = F, sep = "\t")
 
 

diff --git a/Scripts/snakefile_process_IRMA_SNPs.smk b/Scripts/snakefile_process_IRMA_SNPs.smk
@@ -41,7 +41,6 @@ rule fastp_process:
         " --out1 {output[0]} --out2 {output[1]}"
         " --length_required 60 --low_complexity_filter --complexity_threshold 30"
         " --trim_poly_x --correction --detect_adapter_for_pe"
-        " --dedup dup_calc_accuracy 5"
         " --html logs/fastp-{wildcards.sample}.html --json logs/fastp-{wildcards.sample}.json --compression 8"
         " report_title {wildcards.sample}"
 

diff --git a/Scripts/snakefile_process_SNPs.smk b/Scripts/snakefile_process_SNPs.smk
@@ -40,7 +40,6 @@ rule fastp_process:
         " --out1 {output[0]} --out2 {output[1]}"
         " --length_required 60 --low_complexity_filter --complexity_threshold 30"
         " --trim_poly_x --correction --detect_adapter_for_pe"
-        " --dedup dup_calc_accuracy 5"
         " --html logs/fastp-{wildcards.sample}.html --json logs/fastp-{wildcards.sample}.json --compression 8"
         " report_title {wildcards.sample}"