missing ALT assembly

rules/run_05_11_21.smk

@@ -135,7 +135,7 @@ def altFile(wildcards):
 	if samples.loc[(wildcards.asmID), "ALT_present"] == True:
 		return os.path.join(config['Results'], "1_evaluation/{asmID}/01_unzipFastas/{asmID}.ALT.fasta")
 	else:
-		return []
+		return os.path.join(workflow.basedir, "scripts/ALT_missing.fasta")
 
 rule merqury:
 	input:
@@ -396,8 +396,8 @@ rule saveConfiguration_and_getKeyValues:
 		echo "$(grep 'NG50' {input.contStats} | awk {{'print $4'}})" >> {params.keyValues}
 		echo "$(grep 'N95' {input.contStats} | awk {{'print $2'}})" >> {params.keyValues}
 		echo "$(grep 'NG95' {input.contStats} | awk {{'print $4'}})" >> {params.keyValues}
-		echo "$(awk {{'print $4'}} {input.qv})" >> {params.keyValues}
-		echo "$(awk {{'print $5'}} {input.completeness})" >> {params.keyValues}
+		echo "$(awk {{'print $4'}} {input.qv})" | head -n 1 >> {params.keyValues}
+		echo "$(awk {{'print $5'}} {input.completeness})" | head -n 1 >> {params.keyValues}
 		echo "$(grep 'C:' {input.busco} | awk -F'[:\[,]' {{'print $2'}})" >> {params.keyValues}
 		echo "$(grep 'C:' {input.busco} | awk -F'[:\[,]' {{'print $4'}})" >> {params.keyValues}
 		dos2unix {params.keyValues}
@@ -503,10 +503,10 @@ rule aggregateAllAssemblies:
 		sampleSheet= config['samplesTSV'],
 		config=os.path.join(workflow.basedir, "configuration/config.yaml")
 	output:
-		results=os.path.join(config['Results'],"1_evaluation/Combined_Results_FULLTABLE.tsv"),
+		results=os.path.join(config['Results'],"1_evaluation/finalResults/Combined_Results_FULLTABLE.tsv"),
 #		rows=os.path.join(config['Results'],"allAssemblies_keyResults/aggregate_rows.tsv"),
-		newSampleSheet=os.path.join(config['Results'],"1_evaluation/savedSampleSheet.tsv"),
-		newConfigFile=os.path.join(config['Results'],"1_evaluation/savedConfig.yaml")
+		newSampleSheet=os.path.join(config['Results'],"1_evaluation/finalResults/savedSampleSheet.tsv"),
+		newConfigFile=os.path.join(config['Results'],"1_evaluation/finalResults/savedConfig.yaml")
 	shell:
 		"""
 		cp {input.sampleSheet} {output.newSampleSheet}
@@ -563,28 +563,50 @@ rule makeReport:
 # 		awk '{{sub("PLACEHOLDER","{input[0]}")}}1' {input.landingPage} > {output[0]}
 # 		"""
 
+rule addFullTable:
+	input:
+		results=os.path.join(config['Results'],"1_evaluation/finalResults/Combined_Results_FULLTABLE.tsv")
+	output:
+		os.path.join(config['Results'],"1_evaluation/finalResults/FullTableMarkdown.md")
+	run:
+		import pandas as pd
+		from tabulate import tabulate
+		samples=pd.read_csv(input.results, dtype=str, index_col=0, delim_whitespace=True, skip_blank_lines=True)
+		with open(output[0], "w") as out:
+			print("", file=out)
+			print("\\onecolumn", file=out)
+			print("", file=out)
+			print("\\tiny", file=out)
+			print(tabulate(samples, headers='keys',tablefmt="pipe", showindex=True), file=out)
+			print("", file=out)
 
 rule aggregateReport:
 	input:
 		indivMD=[expand(os.path.join(config['Results'],"1_evaluation/{asmID}/06_keyResults/{asmID}_k{kmer}_markdownForReport.md"), asmID=key, kmer=value4) for key, [value1, value2, value3, value4, value5, value6, value7, value8] in testDict.items()],
-		landingPage=os.path.join(workflow.basedir, "scripts/reportLandingPage.md")
+		landingPage=os.path.join(workflow.basedir, "scripts/reportLandingPage.md"),
+		endTableMD=os.path.join(config['Results'],"1_evaluation/finalResults/FullTableMarkdown.md")
 	output:
-		os.path.join(config['Results'],"1_evaluation/FullMarkdown.md")
+		os.path.join(config['Results'],"1_evaluation/finalResults/FullMarkdown.md")
 	shell:
 		"""
-		cat {input.landingPage} > {output}
-		cat {input.indivMD} >> {output}
+		cat {input.landingPage} {input.indivMD} {input.endTableMD} >> {output}
 		"""
 
+
+
+
+
+
 rule makePDF:
 	input:
-		os.path.join(config['Results'],"1_evaluation/FullMarkdown.md")
+		os.path.join(config['Results'],"1_evaluation/finalResults/FullMarkdown.md")
 	output:
-		os.path.join(config['Results'],"1_evaluation/FULL_Report_PDF.pdf")
+		os.path.join(config['Results'],"1_evaluation/finalResults/FULL_Report_PDF.pdf")
 	shell:
 		"""
 		pandoc -o {output} {input}
 		"""
+
 		# 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" > {output.rows}
 		# paste -d'\t' {output.rows} {input.allResults} > {output.results}
 		# awk '{print $1"\t"$3"\t"$5}' {output.results} | column -t {output.results}