first test salmoon

mspodda · May 24, 2024 · 9c242d8 · 9c242d8
1 parent 075051d
commit 9c242d8
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Showing 8 changed files with 1,146 additions and 27 deletions.
diff --git a/config/config_final.yml b/config/config_final.yml
@@ -1,5 +1,5 @@
 # options
-workflow_type: "custom_module"  # Options: "polyA_module", "salmon_module", "custom_module", "custom_and_salmon_modules"
+workflow_type: "salmon_module"  # Options: "polyA_module", "salmon_module", "custom_module", "custom_and_salmon_modules"
 freeze: GRCh38.primary_assembly.genome      # genome version
 
 ############################################################
@@ -39,7 +39,7 @@ reference:
   fasta:
     GRCh38.primary_assembly.genome: $refdir/chr7.fa
   fasta_salmon:
-    GRCh38.primary_assembly.genome: $refdir/gencode.v46.transcripts.fa
+    GRCh38.primary_assembly.genome: $refdir/BRAF_transcripts.fa
   gtf:
     GRCh38.primary_assembly.genome: $refdir/chr7.gtf
   gtf_personal:

diff --git a/test_data/BRAF_transcripts.fa b/test_data/BRAF_transcripts.fa
diff --git a/workflow/R/R_salmon.R b/workflow/R/R_salmon.R
@@ -1,7 +1,6 @@
 setwd(final_output)
-source("config_all.R")
+source("/home/runner/work/isoworm/isoworm/workflow/R/config_all.R")
 lapply(my_packages, require, character.only = TRUE)
-
 ### 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)

diff --git a/workflow/R/config_all.R b/workflow/R/config_all.R
@@ -39,9 +39,9 @@ results_dir <- "/home/runner/work/isoworm/isoworm/results"
 polyA_bam_dir <- ""
 final_output <- "/home/runner/work/isoworm/isoworm/workflow/R"
 ## total salmon
-indexDir <- file.path("")
-fasta <- file.path("")
-gtf   <- file.path("")
+indexDir <- file.path("/home/runner/work/isoworm/isoworm/test_data/salmon_index_v43")
+fasta <- file.path("/home/runner/work/isoworm/isoworm/test_data/BRAF_transcripts.fa")
+gtf   <- file.path("/home/runner/work/isoworm/isoworm/test_data/chr7.gtf")
 
 ## functions
 data_summary <- function(x) {

diff --git a/workflow/util/__pycache__/varsub.cpython-311.pyc b/workflow/util/__pycache__/varsub.cpython-311.pyc
diff --git a/workflow/util/__pycache__/varsub.cpython-312.pyc b/workflow/util/__pycache__/varsub.cpython-312.pyc
diff --git a/workflow/util/script.sh b/workflow/util/script.sh
@@ -1,2 +1,2 @@
-cd results/fastq/$1
+cd results/lung/fastq/$1
 ffq --ftp $1 | grep -Eo '"url": "[^"]*"' | grep -o ftp.sra.*$ | sed 's/.$//' | xargs -n 1 curl -O -C - --silent --show-error
diff --git a/workflow/util/star.sh b/workflow/util/star.sh