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Commit 6480bd41 authored by james94's avatar james94
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path error

parent 7924a1ee
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...@@ -338,7 +338,7 @@ rule assemblyStats: ...@@ -338,7 +338,7 @@ rule assemblyStats:
rule saveConfiguration_and_getKeyValues: rule saveConfiguration_and_getKeyValues:
input: input:
checkLog=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/logs/" + "{sample}" + "_merq.spectra-cn.log"), 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"), 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"), 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"), busco=os.path.join(config['Results'], "{sample}" + "/1_busco4/short_summary.specific." + buscoDataBaseName + "_odb10." + "{sample}" + ".txt"),
...@@ -350,7 +350,7 @@ rule saveConfiguration_and_getKeyValues: ...@@ -350,7 +350,7 @@ rule saveConfiguration_and_getKeyValues:
scaffStats=os.path.join(config['Results'],"{sample}" + "/4_assemblyStats/{sample}_scaffold_stats.tsv"), 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"), 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"), # 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: params:
# sampleSheet= config['samplesTSV'], # sampleSheet= config['samplesTSV'],
# config=os.path.join(workflow.basedir, "configuration/config.yaml"), # config=os.path.join(workflow.basedir, "configuration/config.yaml"),
...@@ -430,7 +430,7 @@ rule aggregateAllAssemblies: ...@@ -430,7 +430,7 @@ rule aggregateAllAssemblies:
cp {input.config} {output.newConfigFile} 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" | \ 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} | \ 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} column -t > {output.results}
printf "All assembly evaluation results aggregated successfully. Please find these results at {output.results}" printf "All assembly evaluation results aggregated successfully. Please find these results at {output.results}"
""" """
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