From 438508189cb2a2e4a6cc45fdcdff4319ca5e2e6f Mon Sep 17 00:00:00 2001
From: "katarzyna.otylia.sikora@gmail.com" <sikora@maximus.ie-freiburg.mpg.de>
Date: Wed, 10 Apr 2024 11:57:49 +0200
Subject: [PATCH] deseq2 salmon

---
 .../shared/rules/DESeq2.singleComp.snakefile  | 41 ++++++-------------
 1 file changed, 12 insertions(+), 29 deletions(-)

diff --git a/snakePipes/shared/rules/DESeq2.singleComp.snakefile b/snakePipes/shared/rules/DESeq2.singleComp.snakefile
index c62349da9..2e506fd5b 100644
--- a/snakePipes/shared/rules/DESeq2.singleComp.snakefile
+++ b/snakePipes/shared/rules/DESeq2.singleComp.snakefile
@@ -52,23 +52,14 @@ rule DESeq2_Salmon_basic:
         fdr = fdr,
         importfunc = os.path.join(maindir, "shared", "rscripts", "DE_functions.R"),
         allele_info = 'FALSE',
-        tx2gene_file = "Annotation/genes.filtered.t2g",
+        tx2gene_file = os.path.join(outdir,"Annotation/genes.filtered.t2g"),
         rmdTemplate = os.path.join(maindir, "shared", "rscripts", "DESeq2Report.Rmd"),
-        formula = config["formula"]
+        formula = config["formula"],
+        counts_table = lambda wildcards,input: os.path.join(outdir,input.counts_table),
+        symbol_file = lambda wildcards,input: os.path.join(outdir,input.symbol_file)
     conda: CONDA_RNASEQ_ENV
-    shell:
-        "cd {params.outdir} && "
-        "Rscript {params.script} "
-        "{input.sampleSheet} " # 1
-        "../{input.counts_table} " # 2
-        "{params.fdr} " # 3
-        "../{input.symbol_file} " # 4
-        "{params.importfunc} " # 5
-        "{params.allele_info} " # 6
-        "../{input.tx2gene_file} " # 7
-        "{params.rmdTemplate} " # 8
-        "{params.formula} " # 9
-        " > ../{log.out} 2> ../{log.err}"
+    script: "{params.script}"
+
 
 rule DESeq2_Salmon_allelic:
     input:
@@ -89,18 +80,10 @@ rule DESeq2_Salmon_allelic:
         fdr = fdr,
         importfunc = os.path.join(maindir, "shared", "rscripts", "DE_functions.R"),
         allele_info = 'TRUE',
-        tx2gene_file = "Annotation/genes.filtered.t2g",
-        rmdTemplate = os.path.join(maindir, "shared", "rscripts", "DESeq2Report.Rmd")
+        tx2gene_file = os.path.join(outdir,"Annotation/genes.filtered.t2g"),
+        rmdTemplate = os.path.join(maindir, "shared", "rscripts", "DESeq2Report.Rmd"),
+        formula = config["formula"],
+        counts_table = lambda wildcards,input: os.path.join(outdir,input.counts_table),
+        symbol_file = lambda wildcards,input: os.path.join(outdir,input.symbol_file)
     conda: CONDA_RNASEQ_ENV
-    shell:
-        "cd {params.outdir} && "
-        "Rscript {params.script} "
-        "{input.sampleSheet} " # 1
-        "../{input.counts_table} " # 2
-        "{params.fdr} " # 3
-        "../{input.symbol_file} " # 4
-        "{params.importfunc} " # 5
-        "{params.allele_info} " # 6
-        "../{input.tx2gene_file} " # 7
-        "{params.rmdTemplate} " # 8
-        " > ../{log.out} 2> ../{log.err}"
+    script: "{params.script}"