second test salmon

mspodda · May 24, 2024 · 8611e40 · 8611e40
1 parent 9c242d8
commit 8611e40
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/workflow/snakefile_final.smk b/workflow/snakefile_final.smk
@@ -275,8 +275,8 @@ rule stringtie_count:
 
 rule salmon_quant:
         input:
-            f1 = config['datadirs']['fastq'] + "/{file}/" + "{file}_1.fastq.gz",
-            f2 = config['datadirs']['fastq'] + "/{file}/" + "{file}_2.fastq.gz",
+            f1 = config['datadirs']['fastq'] + "/{file}/" + "{file}_R1.fq",
+            f2 = config['datadirs']['fastq'] + "/{file}/" + "{file}_R2.fq",
         output:
             salmon_sf = config['datadirs']['salmon'] + "/{file}/"  + "quant.sf"
         params:

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