test boh

mspodda · May 22, 2024 · de1d96a · de1d96a
1 parent c156c7b
commit de1d96a
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Showing 3 changed files with 6 additions and 7 deletions.
diff --git a/R/config_all.R b/R/config_all.R
@@ -34,14 +34,14 @@ group.colors_plot <- c()
 group.colors_pie_chart <- c()
 
 ## directories
-txt_samples <- "../test_data"
-results_dir <- "../results"
+txt_samples <- "../../test_data"
+results_dir <- "../../results"
 polyA_bam_dir <- ""
 final_output <- "R"
 ## total salmon
-indexDir <-file.path("../results/salmon_index_v43/")
-fasta <- file.path("../results/salmon_index_v43/")
-gtf   <- file.path("../results/salmon_index_v43/")
+indexDir <- file.path("../../results/salmon_index_v43/")
+fasta <- file.path("../../results/salmon_index_v43/")
+gtf   <- file.path("../../results/salmon_index_v43/")
 
 ## functions
 data_summary <- function(x) {

diff --git a/workflow/snakefile_final.smk b/workflow/snakefile_final.smk
@@ -77,7 +77,6 @@ rule STAR_index:
         config['conda']['STAR']
     threads: 2
     shell:
-        'mkdir {output.genomedir} && '
         '{params.star} --runThreadN {threads} '
         '--runMode genomeGenerate '
         '--readFilesCommand zcat '

diff --git a/workflow/util/script.sh b/workflow/util/script.sh
@@ -1,2 +1,2 @@
-cd ../../results/$1
+cd results/fastq/$1
 ffq --ftp $1 | grep -Eo '"url": "[^"]*"' | grep -o ftp.sra.*$ | sed 's/.$//' | xargs wget -q -c