rule name changes

SUBMIT_CONFIG/slurm/config.yaml

@@ -7,9 +7,9 @@ cluster:
     --qos={resources.qos}
     --cpus-per-task={threads}
     --mem={resources.mem_mb}
-    --job-name=GEP.{rule}.{wildcards}.%j
-    --output=slurm_logs/{rule}/{wildcards}.%j.out
-    --error=slurm_logs/{rule}/{wildcards}.%j.err
+    --job-name=GEP.{rule}.%j
+    --output=slurm_logs/{rule}/%j.out
+    --error=slurm_logs/{rule}/%j.err
     --time={resources.time}
 
 

Snakefile

@@ -201,9 +201,8 @@ elif set(['ID',	'ASM_LEVEL', 'PRI_asm', 'ALT_asm',	'merylDB',	'merylDB_kmer', 'g
 	dictSamples=samples.T.to_dict('list')
 
 	ruleAllQCFiles=[]
-	ruleAll=expand(os.path.join(config['Results'],"1_evaluation/{asmID}/KEY_RESULTS/{asmID}_aggregatedResults.tsv"), asmID=list(dictSamples.keys())),\
-	 		os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS.tsv"), \
-			os.path.join(config['Results'],"1_evaluation/finalResults/FULL_REPORT.pdf")
+	ruleAll=expand(os.path.join(config['Results'],"1_evaluation/{asmID}/KEY_RESULTS/{asmID}_aggregatedSTATS.tsv"), asmID=list(dictSamples.keys())),\
+			os.path.join(config['Results'],"1_evaluation/finalResults/FINAL_REPORT.pdf")
 
 
 ###  DOWNLOAD BUSCO LINEAGE (IF IT DOESN'T ALREADY EXIST)  ####
@@ -258,7 +257,7 @@ elif set(['ID',	'ASM_LEVEL', 'PRI_asm', 'ALT_asm',	'merylDB',	'merylDB_kmer', 'g
 			raise ValueError("Error - could not identify lineage please check busco site for a correct prefix")
 
 else:
-	raise ValueError('Sample Sheet for not recognised. Please make sure you are using the correct sample sheet')
+	raise ValueError('Sample Sheet not recognised. Please make sure you are using the correct sample sheet')
 
 
 

rules/build_illumina.smk

@@ -251,7 +251,6 @@ rule merylCount_R1_illumina:
 		os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
 	shell:
 		"""
-		export OMP_NUM_THREADS={threads}
 		(meryl count k={params.kmer} threads={threads} {input.read1} output {output}) &> {log}
 		"""
 
@@ -275,7 +274,6 @@ rule merylCount_R2_illumina:
 		os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
 	shell:
 		"""
-		export OMP_NUM_THREADS={threads}
 		(meryl count k={params.kmer} threads={threads} {input.read2} output {output}) &> {log}
 		"""
 
@@ -306,7 +304,6 @@ rule merylUnion_illumina:
 		os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
 	shell:
 		"""
-		export OMP_NUM_THREADS={threads}
 		(meryl union-sum {input.read1} {input.read2} output {output}) &> {log}
 		rm -r {params.removeReadDIR_trimmed}
 		rm -r {params.removeReadDIR_unzipped}

rules/evaluate.smk

@@ -5,24 +5,22 @@ def merylDB(wildcards):
 	return samples.loc[(wildcards.asmID), "merylDB"]
 
 
-localrules: symlink_UnzippedFastq_R1_HiC, 						\
- 			symlink_UnzippedFastq_R2_HiC, 						\
-			symlink_UnzippedFasta_PRI, 					\
-			symlink_UnzippedFasta_ALT, 					\
-			# symlinkMerylDB, 							\
-#			moveBuscoOutputs, 							\
-			copyKeyResults_GenomeScope2Profiles, 	\
-			copyKeyResults, 		\
-			saveConfigurationAndSampleSheet_createComparisonTablesTSV, 					\
-			IndividualKeyResults_createMD, 								\
-			PretextMaps_createMD, 							\
-			ComparisonTables_createMD, 								\
-			ReportWithoutComparisonTables_createMD, 							\
-			ReportWithoutComparisonTables_createPDF,			\
-			ComparisonTablesColoured_createHTML, 			\
-			ComparisonTables_createPDF,		\
-			ComparisonTablesGradient_createHTML,			\
-			COMBINE_ALL_PDFS
+localrules: symlink_UnzippedFastq_R1_HiC, 					\
+ 			symlink_UnzippedFastq_R2_HiC, 					\
+			symlink_UnzippedFasta_PRI, 						\
+			symlink_UnzippedFasta_ALT, 						\
+			KeyResults_GenomescopeProfiles, 				\
+			KeyResults, 									\
+			Tables_TSV, 									\
+			IndividualResults_md, 							\
+			PretextMaps_md, 								\
+			Table_md, 										\
+			Reports_md, 									\
+			Reports_pdf,									\
+			ColouredTable_html, 							\
+			HeatmapTable_html,			\
+			BothTables_pdf,						\
+			ConcatAll_pdfs
 
 def HiC_R1_gzipped(wildcards):
 	return yesGzip_HiC_R1.loc[(wildcards.asmID), "HiC_R1"]
@@ -533,7 +531,7 @@ rule assemblyStats:
 
 
 
-rule copyKeyResults_GenomeScope2Profiles:
+rule KeyResults_GenomescopeProfiles:
 	input:
 		gscopeSum=os.path.join(config['Results'], "1_evaluation/{asmID}/GENOMESCOPE_PROFILES/{asmID}_k{kmer}_summary.txt"),
 		gscopeLog=os.path.join(config['Results'], "1_evaluation/{asmID}/GENOMESCOPE_PROFILES/{asmID}_k{kmer}_log_plot.png"),
@@ -554,7 +552,7 @@ rule copyKeyResults_GenomeScope2Profiles:
 
 
 
-rule copyKeyResults:
+rule KeyResults:
 	input:
 		gscopeSum=lambda wildcards: expand(os.path.join(config['Results'], "1_evaluation/{asmID}/GENOMESCOPE_PROFILES/{asmID}_k{kmer}_summary.txt"), asmID=wildcards.asmID, kmer=dictSamples[wildcards.asmID][4]),
 		# gscopeLog=lambda wildcards: expand(os.path.join(config['Results'], "1_evaluation/{asmID}/GENOMESCOPE_PROFILES/{asmID}_k{kmer}_log_plot.png"), asmID=wildcards.asmID, kmer=dictSamples[wildcards.asmID][4]),
@@ -628,7 +626,7 @@ rule copyKeyResults:
 		rm {params.rowNames} {params.keyValues}
 		"""
 
-rule saveConfigurationAndSampleSheet_createComparisonTablesTSV:
+rule Tables_TSV:
 	input:
 		allResults=expand(os.path.join(config['Results'],"1_evaluation/{asmID}/KEY_RESULTS/{asmID}_aggregatedSTATS.tsv"), asmID=list(dictSamples.keys())),
 		sampleSheet= config['samplesTSV'],
@@ -650,7 +648,7 @@ rule saveConfigurationAndSampleSheet_createComparisonTablesTSV:
 		sed -i 's/,//g' {output.results}
 		"""
 
-rule IndividualKeyResults_createMD:
+rule IndividualResults_md:
 	input:
 		os.path.join(config['Results'],"1_evaluation/{asmID}/KEY_RESULTS/{asmID}_aggregatedSTATS.tsv"),
 		lambda wildcards: expand(os.path.join(config['Results'], "1_evaluation/{asmID}/KEY_RESULTS/{asmID}_k{kmer}_log_plot.png"),asmID=wildcards.asmID, kmer=dictSamples[wildcards.asmID][4]),
@@ -673,7 +671,7 @@ rule IndividualKeyResults_createMD:
 
 
 
-rule PretextMaps_createMD:
+rule PretextMaps_md:
 	input:
 		PretextMap=os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.COMBINED.FILTERED_FullMap.png")
 	output:
@@ -686,7 +684,7 @@ rule PretextMaps_createMD:
 	script:
 		os.path.join(workflow.basedir, "scripts/report/pretextMapsToMarkdown.py")
 
-rule ComparisonTables_createMD:
+rule Table_md:
 	input:
 		results=os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS.tsv")
 	output:
@@ -697,7 +695,7 @@ rule ComparisonTables_createMD:
 	script:
 		os.path.join(workflow.basedir, "scripts/report/addFullTableForReport.py")
 
-rule ComparisonTablesColoured_createHTML:
+rule ColouredTable_html:
 	input:
 		os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS_roundedMB.tsv")
 	params:
@@ -714,7 +712,7 @@ rule ComparisonTablesColoured_createHTML:
 	script:
 		os.path.join(workflow.basedir, "scripts/compare_results/fullTable_heatmap_external.R")
 
-rule ComparisonTablesGradient_createHTML:
+rule HeatmapTable_html:
 	input:
 		os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS_roundedMB.tsv")
 	params:
@@ -731,7 +729,7 @@ rule ComparisonTablesGradient_createHTML:
 	script:
 		os.path.join(workflow.basedir, "scripts/compare_results/fullTable_heatmap_internalComparison.R")
 
-rule ComparisonTables_createPDF:
+rule BothTables_pdf:
 	input:
 		coloured=os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS_COLOURED.html"),
 		gradient=os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS_GRADIENT.html")
@@ -756,7 +754,7 @@ rule ComparisonTables_createPDF:
 		-o {output.gradient} --pdf-engine=wkhtmltopdf --pdf-engine-opt="-O" --pdf-engine-opt="Landscape" {input.gradient}) &>> {log}
 		"""
 
-rule ReportWithoutComparisonTables_createMD:
+rule Reports_md:
 	input:
 		indivMD=[expand(os.path.join(config['Results'],"1_evaluation/{asmID}/KEY_RESULTS/{asmID}_k{kmer}_markdownForReport.md"), asmID=key, kmer=value5) for key, [value1, value2, value3, value4, value5, value6, value7, value8, value9, value10, value11, value12, value13, value14, value15, value16] in dictSamples.items()],
 		landingPage=os.path.join(workflow.basedir, "scripts/report/reportLandingPage.md"),
@@ -775,7 +773,7 @@ rule ReportWithoutComparisonTables_createMD:
 #		cat {input.landingPageTABLE} {input.endTableMD} >> {output.endTableMD}
 
 
-rule ReportWithoutComparisonTables_createPDF:
+rule Reports_pdf:
 	input:
 		md_report=os.path.join(config['Results'],"1_evaluation/finalResults/ALL_individual_REPORTS.md"),
 #		md_comparison_table=os.path.join(config['Results'],"1_evaluation/finalResults/FullTableMarkdown_wPreamble.md")
@@ -797,7 +795,7 @@ rule ReportWithoutComparisonTables_createPDF:
 		"""
 	#	(pandoc -o {output.pdf_comparison_table} {input.md_comparison_table} --pdf-engine=tectonic) &>> {log}
 
-rule COMBINE_ALL_PDFS:
+rule ConcatAll_pdfs:
 	input:
 		pdf_report=os.path.join(config['Results'],"1_evaluation/finalResults/ALL_individual_REPORTS.pdf"),
 		coloured=os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS_COLOURED.pdf"),
@@ -807,7 +805,7 @@ rule COMBINE_ALL_PDFS:
 		pdf_report=os.path.join(config['Results'],"1_evaluation/finalResults/FINAL_REPORT.pdf"),
 #		pdf_comparison_table=os.path.join(config['Results'],"1_evaluation/finalResults/FULL_TABLE_PDF.pdf")
 	log:
-		os.path.join(config['Results'], "1_evaluation/logs/COMBINE_ALL_PDFS.log")
+		os.path.join(config['Results'], "1_evaluation/logs/ConcatAll_pdfs.log")
 	conda:
 		os.path.join(workflow.basedir, "envs/AUXILIARY_PYTHON_SCRIPTS.yaml")
 	# threads: