test salmon dai

mspodda · May 24, 2024 · 4c12407 · 4c12407
1 parent 556ff83
commit 4c12407
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/test_data/chr7.fa.gz b/test_data/chr7.fa.gz
diff --git a/workflow/R/R_salmon.R b/workflow/R/R_salmon.R
@@ -1,6 +1,6 @@
-setwd(final_output)
 source("/home/runner/work/isoworm/isoworm/workflow/R/config_all.R")
 lapply(my_packages, require, character.only = TRUE)
+library(data.table)
 ### Create a list with all txt files containing the samples for each tissues line 
 ### Extract all samples from the txt list files for each tissues line typology  
 setwd(txt_samples)
@@ -83,7 +83,7 @@ db_ratio$group <- NA
 db_ratio$IDS   <- NA
 tissues_numbers  <- c()
 for (i in 1:length(samples_typologies)){
-  tissues_numbers  <- c(tissues_numbers,as.integer(count(get(paste0(samples_typologies[i],"_BRAF_results")))))
+  tissues_numbers  <- c(tissues_numbers,nrow(get(paste0(samples_typologies[i],"_BRAF_results"))))
 }
 
 count  = 1

diff --git a/workflow/snakefile_final.smk b/workflow/snakefile_final.smk
@@ -296,7 +296,7 @@ rule salmon_quant:
         priority: 60
         shell:
             """
-            {params.salmon} quant -l {params.libtype} -i {params.salmon_index} -1 {input.f1} -2 {input.f2} -p {threads} -o {params.outdir_all_salmon}
+            {params.salmon} quant --minAssignedFrags 9 -l {params.libtype} -i {params.salmon_index} -1 {input.f1} -2 {input.f2} -p {threads} -o {params.outdir_all_salmon}
             """
-Original file line number
+Diff line change
@@ Expand Up / @@ -296,7 +296,7 @@ rule salmon_quant: @@
             priority: 60
             shell:
                 """
-                {params.salmon} quant -l {params.libtype} -i {params.salmon_index} -1 {input.f1} -2 {input.f2} -p {threads} -o {params.outdir_all_salmon}
+                {params.salmon} quant --minAssignedFrags 9 -l {params.libtype} -i {params.salmon_index} -1 {input.f1} -2 {input.f2} -p {threads} -o {params.outdir_all_salmon}
                 """
@@ Expand Down @@