path error

rules/rulesNew.smk

@@ -338,7 +338,7 @@ rule assemblyStats:
 rule saveConfiguration_and_getKeyValues:
 	input:
 		checkLog=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/logs/" + "{sample}" + "_merq.spectra-cn.log"),
-		gscopeSum=os.path.join(config['Results'], "{sample}" +"/2_genomescopeProfile/" + "{sample}" + "_summary.txt"),
+		gscopeSum=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_summary.txt"),
 		gscopeLog=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_log_plot.png"),
 		gscopeLin=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_linear_plot.png"),
 		busco=os.path.join(config['Results'], "{sample}" + "/1_busco4/short_summary.specific." + buscoDataBaseName + "_odb10." + "{sample}" + ".txt"),
@@ -350,7 +350,7 @@ rule saveConfiguration_and_getKeyValues:
 		scaffStats=os.path.join(config['Results'],"{sample}" + "/4_assemblyStats/{sample}_scaffold_stats.tsv"),
 		contStats=os.path.join(config['Results'],"{sample}" + "/4_assemblyStats/{sample}_contig_stats.tsv"),
 #		os.path.join(config['Results'],"{sample}" + "/QVstats_merylAndMerqury/logs/" + "{sample}" + "_meryl.log"),
-		multiqc=os.path.join(config['Results'],"{sample}/0_qualityControl/multiqc/{sample}_multiqc_report.html")
+		multiqc=os.path.join(config['Results'],"{sample}/0_qualityControl/02_multiqc/{sample}_multiqc_report.html")
 	params:
 		# sampleSheet= config['samplesTSV'],
 		# config=os.path.join(workflow.basedir, "configuration/config.yaml"),
@@ -430,7 +430,7 @@ rule aggregateAllAssemblies:
 		cp {input.config} {output.newConfigFile}
 		echo -e "Assembly\nsize_estimate\nmax_heterozygosity\nqv_score\nN50_length\nNG50_length\nN95_length\nNG95_length\nN100_length\nNG100_length\ntotal_num_bases\ntotal_num_scaffolds" | \
 		paste -d'\t' - {input.allResults} | \
-		awk -F'\t' '{s="";for (i=1;i<=NF;i+=2) {s=s?s FS $i:$i} print s}' | \
+		awk -F'\t' '{{s="";for (i=1;i<=NF;i+=2) {{s=s?s FS $i:$i}} print s}}' | \
 		column -t > {output.results}
 		printf "All assembly evaluation results aggregated successfully.  Please find these results at {output.results}"
 		"""