Cleaning up

config/config.yaml

@@ -12,11 +12,11 @@ workdir: "/scratch/sjannalda/projects/ArnicaProcessing"
 
 # Samples to analyze
 samples:
-    #spain1: /remote/trove/bgbm/baobab/2018_ArnicaSNP/spain/FASTQ/HFYM3DSX7_1_379UDI-idt-UMI
+    spain1:  /scratch/reichel/pipelinetest/Spain/FASTQ/HFYM3DSX7_1_379UDI-idt-UMI
     #ERR8268641: /scratch/sjannalda/bgbm/data/DownloadedData/ERR8268641/test/ERR8268641
-    SRR17032099: /scratch/sjannalda/projects/PlastidPipelineTesting/rawdata/SRR17032099/SRR17032099
+    #SRR17032099: /scratch/sjannalda/projects/PlastidPipelineTesting/rawdata/SRR17032099/SRR17032099
     #SRR12917849: /scratch/sjannalda/projects/PlastidPipelineTesting/rawdata/SRR12917849/SRR12917849
-    SRR12917857: /scratch/sjannalda/projects/PlastidPipelineTesting/rawdata/SRR12917857/SRR12917857
+    #SRR12917857: /scratch/sjannalda/projects/PlastidPipelineTesting/rawdata/SRR12917857/SRR12917857
     #ERR5529317: /scratch/sjannalda/projects/PlastidPipelineTesting/rawdata/ERR5529317/ERR5529317
     #ERR5529436: /scratch/sjannalda/projects/PlastidPipelineTesting/rawdata/ERR5529436/ERR5529436
     #ERR5554746: /scratch/sjannalda/projects/PlastidPipelineTesting/rawdata/ERR5554746/ERR5554746

workflow/Snakefile

@@ -3,16 +3,17 @@ import os
 workdir:config["workdir"]
 
 for sample in config["samples"]:
-	if os.path.exists("%s_1.fq" %config["samples"][sample]):
-		end=".fq"
-	elif  os.path.exists("%s_1.fq.gz" %config["samples"][sample]):
+	if  os.path.exists("%s_1.fq.gz" %config["samples"][sample]):
 		end=".fq.gz"
-	elif  os.path.exists("%s_1.fastq" %config["samples"][sample]):
-		end=".fastq"
 	elif os.path.exists("%s_1.fastq.gz" %config["samples"][sample]):
 		end=".fastq.gz"
+	elif  os.path.exists("%s_1.fastq" %config["samples"][sample]):
+		end=".fastq"
+	elif os.path.exists("%s_1.fq" %config["samples"][sample]):
+		end=".fq"
 	else:
 		raise Exception("Input data %s not in proper format (either '.fq', '.fq.gz', '.fastq', or '.fastq.gz') or does not exist." %sample)
+	print(end)
 
 def allInputFunction(wildcards):
 	output = []
@@ -24,7 +25,6 @@ def allInputFunction(wildcards):
 
 	output += expand("{sample}/01_data/{sample}.trimmed.qc.html",sample=config["samples"])
 
-
 
 	if (config["Standardization"]):
 		output += expand("{sample}/03_annotation/{sample}.standardardized.filt.gb", sample=config["samples"])

workflow/rules/01_Processing.smk

@@ -34,7 +34,7 @@ rule SortReads:
 		read="{sample}/01_data/{sample}_{read}.trimmed.sorted.fastq.gz"
 	resources:
 		mem_mb=20000,
-		time="0-01:00:00"
+		time="0-03:00:00"
 	envmodules:
 		"bioawk"
 	shell: