From 6480bd41359720affea2a0d35cd31ef0d5d49ff0 Mon Sep 17 00:00:00 2001
From: james94 <james94@mi.fu-berlin.de>
Date: Wed, 24 Feb 2021 18:50:43 +0100
Subject: [PATCH] path error
---
rules/rulesNew.smk | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/rules/rulesNew.smk b/rules/rulesNew.smk
index 13e1386..672e31a 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}"
"""
--
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