diff --git a/rules/evaluate.smk b/rules/evaluate.smk index 18f8313d2d0d77fbb8f60b899f9fb8b5972c1efb..f3a4d3557ae8d48943b3c35d8d6b64b89f13d562 100644 --- a/rules/evaluate.smk +++ b/rules/evaluate.smk @@ -52,7 +52,7 @@ def merylDB(wildcards): return samples.loc[(wildcards.asmID), "merylDB"] -localrules: symlinkUnzippedHiC_R1, symlinkUnzippedHiC_R2, symlinkUnzippedFasta_PRI, symlinkUnzippedFasta_ALT, moveBuscoOutputs, saveConfiguration_and_getKeyValues_kmer, saveConfiguration_and_getKeyValues, aggregateAllAssemblies, makeReport, pretextMaps2md, addFullTable, aggregateReport +localrules: symlinkUnzippedHiC_R1, symlinkUnzippedHiC_R2, symlinkUnzippedFasta_PRI, symlinkUnzippedFasta_ALT, symlinkMerylDB, moveBuscoOutputs, saveConfiguration_and_getKeyValues_kmer, saveConfiguration_and_getKeyValues, aggregateAllAssemblies, makeReport, pretextMaps2md, addFullTable, aggregateReport def HiC_R1_gzipped(wildcards): return yesGzip_HiC_R1.loc[(wildcards.asmID), "HiC_R1"] @@ -419,16 +419,28 @@ def altFile(wildcards): else: return os.path.join(workflow.basedir, "scripts/ALT_missing.fasta") +rule symlinkMerylDB: + input: + merylDB_provided=merylDB + output: + symlink_merylDB=directory(os.path.join(config['Results'], "1_evaluation/{asmID}/04_merquryQVandKAT/merylDB_providedFor_{asmID}.meryl")) + container: + None + shell: + """ + ln -s {input.merylDB_provided} {output.symlink_merylDB} + """ rule merqury: input: assemblyPRI=os.path.join(config['Results'], "1_evaluation/{asmID}/01_unzipFastas/{asmID}.PRI.fasta"), assemblyALT=altFile, - merylDB_provided=merylDB +# merylDB_provided=merylDB + merylDB=os.path.join(config['Results'], "1_evaluation/{asmID}/04_merquryQVandKAT/merylDB_providedFor_{asmID}.meryl") params: outFile= "{asmID}" + "_merqOutput", outPath= os.path.join(config['Results'],"1_evaluation/{asmID}/04_merquryQVandKAT"), - symlink_merylDB=directory(os.path.join(config['Results'], "1_evaluation/{asmID}/04_merquryQVandKAT/merylDB_providedFor_{asmID}.meryl")) +# symlink_merylDB=directory(os.path.join(config['Results'], "1_evaluation/{asmID}/04_merquryQVandKAT/merylDB_providedFor_{asmID}.meryl")) threads: resource['merqury']['threads'] resources: @@ -452,9 +464,9 @@ rule merqury: """ cd {params.outPath} export OMP_NUM_THREADS={threads} - ln -s {input.merylDB_provided} {params.symlink_merylDB} - (merqury.sh {params.symlink_merylDB} {input.assemblyPRI} {input.assemblyALT} {params.outFile}) &> {log} + (merqury.sh {input.merylDB} {input.assemblyPRI} {input.assemblyALT} {params.outFile}) &> {log} """ +# ln -s {input.merylDB_provided} {params.symlink_merylDB} #######################################################################################################################################