diff --git a/rules/rulesNew.smk b/rules/rulesNew.smk index 13e1386aeace9768485c55860c4e5b83fd8132ff..672e31a8dc70601cb6f2dbac7fd88ad96710a2cc 100644 --- a/rules/rulesNew.smk +++ b/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}" """