diff --git a/Snakefile b/Snakefile
index 2ae29b62c71cef5229fe7bce6b291a1af00a7ebf..38c8cf60903985cfb0e32743eb87af627056edb9 100644
--- a/Snakefile
+++ b/Snakefile
@@ -15,6 +15,7 @@ configfile: "configuration/config.yaml"
samples = pd.read_csv(config['samplesTSV'], dtype=str, index_col="assemblyName", delim_whitespace=True, skip_blank_lines=True)
if 'Library_R1' in samples.columns:
+ whichRule = "rules/rulesNew.smk"
samples['combined']=samples['Library_R1'].astype(str)+' '+samples['Library_R2'].astype(str)
samples = samples.drop(columns=['Library_R1','Library_R2'])
samples['est_bp'] = samples['est_bp'].fillna(0)
@@ -34,6 +35,7 @@ if 'Library_R1' in samples.columns:
samples=samples.join(samples6['est_bp'])
# print("The following assemblies will be evaluated: ", list(samples.index))
elif 'preBuiltMerylDatabase' in samples.columns:
+ whichRule = "rules/rulesNew_short.smk"
samples['est_bp'] = samples['est_bp'].fillna(0)
samples["est_bp"] = pd.to_numeric(samples["est_bp"])
# print("The following assemblies will be evaluated: ", list(samples.index))
@@ -107,7 +109,7 @@ if "Results" not in config:
report: "report/workflow.rst"
-include: "rules/rulesNew_short.smk"
+include: whichRule
rule all:
diff --git a/rules/rulesNew.smk b/rules/rulesNew.smk
index c94a9cb6f394c4ad82e1f1b6a3514a9b0dccbdff..7d356edb41a5985097525b7e9ec98e4b33b301e6 100644
--- a/rules/rulesNew.smk
+++ b/rules/rulesNew.smk
@@ -23,13 +23,13 @@ rule trimAdapters:
threads:
8
log:
- os.path.join(config['Results'], "logs/0_qualityControl/{sample}_tGalore.log")
+ os.path.join(config['Results'], "{sample}" + "/0_qualityControl/logs/{sample}_tGalore.log")
priority:
15
conda:
"../envs/pigz.yaml"
shell:
- "(trim_galore -q 5 -j {threads} --dont_gzip --fastqc --length 65 -o {params.base} --paired {params.file}) &> {log}"
+ "(trim_galore -j {threads} --dont_gzip --fastqc --length 65 -o {params.base} --paired {params.file}) &> {log}"
rule multiqc:
input:
@@ -108,7 +108,7 @@ rule busco5:
conda:
"../envs/busco_and_assembly.yaml"
log:
- os.path.join(config['Results'], "logs/1_busco5/{sample}_busco5.log")
+ os.path.join(config['Results'], "{sample}" + "/1_busco5/" + "{sample}" + "/logs/{sample}_busco5.log")
priority:
20
shell:
@@ -147,23 +147,22 @@ rule meryl_R1:
# check = os.path.join(config['Results'], "{sample}" + "/busco5/short_summary.specific." + config['busco5Lineage'] + "_odb10." + "{sample}" + ".txt")
params:
# script = os.path.join(workflow.basedir, "programs/meryl/build/bin/meryl"),
- script = os.path.join(workflow.basedir, "programs/meryl-1.0/Linux-amd64/bin/meryl"),
kmer = 21,
- r1= "{sample}" + "_R1.21.meryl",
path= os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/")
threads:
- workflow.cores * 0.5
+ workflow.cores * 0.25
output:
directory(os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{sample}" + "_R1.21.meryl"))
log:
- os.path.join(config['Results'], "logs/2_merylAndMerq/{sample}_meryl_R1.log")
+ os.path.join(config['Results'], "{sample}" + "/2_QVstats_merylAndMerqury/logs/{sample}_meryl_R1.log")
priority:
10
conda:
- "../envs/merylMerq.yaml"
+ "../envs/merylMerq_2.yaml"
shell:
"""
- ({params.script} count k={params.kmer} threads={threads} {input.read1} output {output}) &> {log}
+ cd {params.path}
+ (meryl count k={params.kmer} threads={threads} {input.read1} output {output}) &> {log}
"""
rule meryl_R2:
@@ -172,23 +171,23 @@ rule meryl_R2:
# check = os.path.join(config['Results'], "{sample}" + "/busco5/short_summary.specific." + config['busco5Lineage'] + "_odb10." + "{sample}" + ".txt")
params:
# script = os.path.join(workflow.basedir, "programs/meryl/build/bin/meryl"),
- script = os.path.join(workflow.basedir, "programs/meryl-1.0/Linux-amd64/bin/meryl"),
kmer = 21,
- r2= "{sample}" + "_R2.21.meryl",
+# r2= "{sample}" + "_R2.21.meryl",
path= os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/")
threads:
- workflow.cores * 0.5
+ workflow.cores * 0.25
output:
directory(os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{sample}" + "_R2.21.meryl")),
log:
- os.path.join(config['Results'], "logs/2_merylAndMerq/{sample}_meryl_R2.log")
+ os.path.join(config['Results'], "{sample}" + "/2_QVstats_merylAndMerqury/logs/{sample}_meryl_R2.log")
priority:
10
conda:
- "../envs/merylMerq.yaml"
+ "../envs/merylMerq_2.yaml"
shell:
"""
- ({params.script} count k={params.kmer} threads={threads} {input.read2} output {output}) &> {log}
+ cd {params.path}
+ (meryl count k={params.kmer} threads={threads} {input.read2} output {output}) &> {log}
"""
rule meryl:
@@ -198,64 +197,65 @@ rule meryl:
# check = os.path.join(config['Results'], "{sample}" + "/busco5/short_summary.specific." + config['busco5Lineage'] + "_odb10." + "{sample}" + ".txt")
params:
# script = os.path.join(workflow.basedir, "programs/meryl/build/bin/meryl"),
- script = os.path.join(workflow.basedir, "programs/meryl-1.0/Linux-amd64/bin/meryl"),
kmer = 21,
# r1= "{sample}" + "_R1.21.meryl",
# r2= "{sample}" + "_R2.21.meryl",
# dB= "{sample}" + "_dB.21.meryl",
- path= os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/{sample}_dB.21.meryl")
+ path= os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/")
threads:
- workflow.cores * 0.5
+ workflow.cores * 0.25
output:
directory(os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{sample}" + "_dB.21.meryl")),
log:
- os.path.join(config['Results'], "logs/2_merylAndMerq/{sample}_meryl_dB.log")
+ os.path.join(config['Results'], "{sample}" + "/2_QVstats_merylAndMerqury/logs/{sample}_meryl_dB.log")
priority:
5
conda:
- "../envs/merylMerq.yaml"
+ "../envs/merylMerq_2.yaml"
shell:
"""
- ({params.script} union-sum {input.read1} {input.read2} threads={threads} output {output}) &> {log}
+ cd {params.path}
+ (meryl union-sum {input.read1} {input.read2} threads={threads} output {output}) &> {log}
"""
+
rule merqury:
input:
- check = os.path.join(config['Results'], "logs/2_merylAndMerq/{sample}_meryl_dB.log"),
assembly=lambda wildcards: samples.at[wildcards.sample, 'assembly_fasta'] \
if wildcards.sample in samples.index else '',
merylDB=os.path.join(config['Results'],"{sample}"+ "/2_QVstats_merylAndMerqury/" + "{sample}" + "_dB.21.meryl")
params:
- script = os.path.join(workflow.basedir, "programs/merqury-1.1/merqury.sh"),
+ # script = os.path.join(workflow.basedir, "programs/merqury-1.1/merqury.sh"),
outFile= "{sample}" + "_merq",
# outFile= os.path.join(config['Results'], "{sample}" +"/QVstats_merylAndMerqury/{sample}_merq"),
# merylPath = os.path.join(workflow.basedir, "programs/meryl/build/bin:$PATH"),
- merylPath = os.path.join(workflow.basedir, "programs/meryl-1.0/Linux-amd64/bin:$PATH"),
+ # merylPath = os.path.join(workflow.basedir, "programs/meryl-1.0/Linux-amd64/bin:$PATH"),
outPath= os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury"),
- export= os.path.join(workflow.basedir, "programs/merqury-1.1")
+ symlink_fasta=os.path.join(config['Results'], "{sample}" + "/{sample}.fasta"),
+ symlink_merylDB=directory(os.path.join(config['Results'], "{sample}" + "/combinedRead1Read2.21.meryl"))
+ # export= os.path.join(workflow.basedir, "programs/merqury-1.1")
threads:
- workflow.cores * 0.5
+ workflow.cores * 0.25
output:
report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.qv"), caption="../report/merqury/qvScore.rst", category="QV Estimate", subcategory="{sample}"),
report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}.spectra-cn.st.png"), caption="../report/merqury/spectra-cn_stacked.rst", category="Copy Number Spectra Plots", subcategory="{sample}"),
report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}.spectra-cn.fl.png"), caption="../report/merqury/spectra-cn_filled.rst", category="Copy Number Spectra Plots", subcategory="{sample}"),
- os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{sample}" + "_dB.21.hist"),
- symlink=os.path.join(config['Results'], "{sample}" + "/{sample}.fasta")
+ os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/combinedRead1Read2.21.hist")
log:
os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/logs/{sample}_merqury.log")
priority:
3
conda:
- "../envs/merylMerq.yaml"
+ "../envs/merylMerq_2.yaml"
shell:
"""
+ ln -s {input.assembly} {params.symlink_fasta}
+ ln -s {input.merylDB} {params.symlink_merylDB}
cd {params.outPath}
- ln -s {input.assembly} {output.symlink}
- export PATH={params.merylPath}
- export MERQURY={params.export}
export OMP_NUM_THREADS={threads}
- (bash {params.script} {input.merylDB} {output.symlink} {params.outFile}) &> {log}
+ (merqury.sh {params.symlink_merylDB} {params.symlink_fasta} {params.outFile}) &> {log}
"""
+
# bash {params.script} {input.merylDB} {params.symlink} {params.outFile}
# """
@@ -265,29 +265,31 @@ rule merqury:
# cd {params.outPath}
# bash {params.script} {input.merylDB} {input.assembly} {params.outFile}
# """
+
rule genomescope2:
input:
- hist=os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{sample}" + "_dB.21.hist"),
+ hist=os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/combinedRead1Read2.21.hist"),
check1=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}.spectra-cn.fl.png"),
check2=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}.spectra-cn.st.png")
params:
outFolder=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/"),
- cpHist=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_dB.21.histo"),
+ cpHist=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/combinedRead1Read2_10k.21.histo"),
findGscope=os.path.join(workflow.basedir)
output:
summary=report(os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_summary.txt"), caption="../report/genomescope/summary.rst", category="Genomescope Profile", subcategory="{sample}"),
logPlot=report(os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_log_plot.png"), caption="../report/genomescope/logplot.rst", category="Genomescope Profile", subcategory="{sample}"),
linearPlot=report(os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_linear_plot.png"), caption="../report/genomescope/linearplot.rst", category="Genomescope Profile", subcategory="{sample}"),
- estimatedSize=temp(os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_sizeEst.txt"))
+ estimatedSize=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_sizeEst.txt")
conda:
"../envs/genomescope.yaml"
shell:
"""
- expand -t 1 {input.hist} > {params.cpHist}
+ head -n 10000 {input.hist} > {params.cpHist}
export genomescope2script=$(find {params.findGscope} -name genomescope2)
Rscript $genomescope2script -i {params.cpHist} -o {params.outFolder} -k 21 -n {wildcards.sample}
grep "Genome Haploid Length" {output.summary} | awk {{'print $6'}} | sed 's/,//g'> {output.estimatedSize}
"""
+ # expand -t 1 {input.hist} > {params.cpHist}
rule assemblyStats:
input:
@@ -299,18 +301,20 @@ rule assemblyStats:
# report(os.path.join(config['Results'],"{sample}" + "/assemblyStats/{sample}_contig_stats.tsv"), caption="../report/assemblystats/{sample}_scaffold_rst.rst", category="Assembly Statistics", subcategory="{sample}"),
scaffStats=report(os.path.join(config['Results'],"{sample}" + "/4_assemblyStats/{sample}_scaffold_stats.tsv"), caption="../report/assemblystats/stats.rst", category="Assembly Statistics", subcategory="{sample}"),
contStats=report(os.path.join(config['Results'],"{sample}" + "/4_assemblyStats/{sample}_contig_stats.tsv"), caption="../report/assemblystats/stats.rst", category="Assembly Statistics", subcategory="{sample}"),
- scaff_rst = temp(os.path.join(workflow.basedir, "report/assemblystats/{sample}_scaffold_rst.rst")),
- contig_rst = temp(os.path.join(workflow.basedir, "report/assemblystats/{sample}_contig_rst.rst"))
+ #scaff_rst = temp(os.path.join(workflow.basedir, "report/assemblystats/{sample}_scaffold_rst.rst")),
+ # contig_rst = temp(os.path.join(workflow.basedir, "report/assemblystats/{sample}_contig_rst.rst"))
params:
script = os.path.join(workflow.basedir, "scripts/stats.py"),
path = os.path.join(config['Results'], "{sample}" + "/4_assemblyStats/"),
filename="{sample}",
- given_size=lambda wildcards: samples.at[wildcards.sample, 'EstimatedSize(bps)'] \
+ given_size=lambda wildcards: samples.at[wildcards.sample, 'est_bp'] \
if wildcards.sample in samples.index else ''
shell:
"""
- python {params.script} {input.assembly} {input.estGenome} {params.filename} {output.scaff_rst} {output.contig_rst} {params.given_size} {output.scaffStats} {output.contStats}
+ python {params.script} {input.assembly} {input.estGenome} {params.filename} {params.given_size} {output.scaffStats} {output.contStats}
"""
+# python {params.script} {input.assembly} {input.estGenome} {params.filename} {output.scaff_rst} {output.contig_rst} {params.given_size} {output.scaffStats} {output.contStats}
+
# estGenomeSize=$( grep 'Genome Haploid Length' {input.estGenome} | awk {{'print $6'}} | sed 's/,//g' )
# rule moveMerqOutput:
@@ -356,18 +360,18 @@ 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/02_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"),
- resultsPath=os.path.join(config['Results'],"{sample}"+ "/5_Key_Results")
+ resultsPath=os.path.join(config['Results'],"{sample}"+ "/5_Key_Results"),
+ keyValues=os.path.join(config['Results'],"{sample}"+ "/5_Key_Results/results_withoutRowNames.tsv"),
+ rowNames=os.path.join(config['Results'],"{sample}"+ "/5_Key_Results/rowNames.tsv"),
# masteraggregate=os.path.join(config['Results'],"{sample}"+ "/keyResults/aggregate.tsv")
output:
# newSampleSheet=os.path.join(config['Results'],"{sample}"+ "/keyResults/savedSampleSheet.tsv"),
# newConfigFile=os.path.join(config['Results'],"{sample}"+ "/keyResults/savedConfig.yaml"),
# merqLog=os.path.join(config['Results'],"logs/2_merylAndMerq/" + "{sample}" + "_merqury.spectra-cn.log"),
- keyValues=temp(os.path.join(config['Results'],"{sample}"+ "/5_Key_Results/aggregate.tsv")),
- rowNames=temp(os.path.join(config['Results'],"{sample}"+ "/5_Key_Results/aggregate_rowNames.tsv")),
keyValuesWithRowNames=os.path.join(config['Results'],"{sample}"+ "/5_Key_Results/{sample}_aggregatedResults.tsv"),
gscopeSum=os.path.join(config['Results'], "{sample}" +"/5_Key_Results/" + "{sample}" + "_gScope_summary.txt"),
gscopeLog=os.path.join(config['Results'], "{sample}" +"/5_Key_Results/" + "{sample}" + "_gScope_log_plot.png"),
@@ -381,7 +385,7 @@ rule saveConfiguration_and_getKeyValues:
scaffStats=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/{sample}_scaffold_stats.tsv"),
contStats=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/{sample}_contig_stats.tsv"),
# os.path.join(config['Results'],"{sample}" + "/QVstats_merylAndMerqury/logs/" + "{sample}" + "_meryl.log"),
- multiqc=os.path.join(config['Results'],"{sample}/5_Key_Results/{sample}_multiqc_report.html")
+# multiqc=os.path.join(config['Results'],"{sample}/5_Key_Results/{sample}_multiqc_report.html")
# aggregateTsv=os.path.join(config['Results'],"{sample}"+ "/individual_aggregated_results/aggregate.tsv")
conda:
"../envs/dos2unix.yaml"
@@ -396,24 +400,29 @@ rule saveConfiguration_and_getKeyValues:
cp {input.spectraFlat} {output.spectraFlat}
cp {input.scaffStats} {output.scaffStats}
cp {input.contStats} {output.contStats}
- cp {input.multiqc} {output.multiqc}
- echo "{wildcards.sample}" >> {output.keyValues}
- echo "$(grep 'Genome Haploid Length' {input.gscopeSum} | awk {{'print $6'}} )" >> {output.keyValues}
- echo "$(grep 'Heterozygous (ab)' {input.gscopeSum} | awk {{'print $4'}})" >> {output.keyValues}
- echo "$(awk {{'print $4'}} {input.qv})" >> {output.keyValues}
- echo "$(grep 'N50' {input.scaffStats} | awk {{'print $2'}})" >> {output.keyValues}
- echo "$(grep 'NG50' {input.scaffStats} | awk {{'print $4'}})" >> {output.keyValues}
- echo "$(grep 'N95' {input.scaffStats} | awk {{'print $2'}})" >> {output.keyValues}
- echo "$(grep 'NG95' {input.scaffStats} | awk {{'print $4'}})" >> {output.keyValues}
- echo "$(grep 'N100' {input.scaffStats} | awk {{'print $2'}})" >> {output.keyValues}
- echo "$(grep 'NG100' {input.scaffStats} | awk {{'print $4'}})" >> {output.keyValues}
- echo "$(grep 'total_bps' {input.scaffStats} | awk {{'print $3'}})" >> {output.keyValues}
- echo "$(grep 'sequence_count' {input.scaffStats} | awk {{'print $2'}})" >> {output.keyValues}
- dos2unix {output.keyValues}
- echo -e "Assembly\nsize_estimate\nmax_heterozygosity\nqv_score\nN50_length\nNG50_length\nN95_length\nNG95_length\nN100_length\nNG100_length\ntotal_num_bases\ntotal_num_scaffolds" > {output.rowNames}
- paste -d'\t' {output.rowNames} {output.keyValues} > {output.keyValuesWithRowNames}
+ echo "{wildcards.sample}" >> {params.keyValues}
+ echo "$(grep 'Genome Haploid Length' {input.gscopeSum} | awk {{'print $6'}} )" >> {params.keyValues}
+ echo "$(grep 'Heterozygous (ab)' {input.gscopeSum} | awk {{'print $4'}})" >> {params.keyValues}
+ echo "$(awk {{'print $4'}} {input.qv})" >> {params.keyValues}
+ echo "$(grep 'N50' {input.scaffStats} | awk {{'print $2'}})" >> {params.keyValues}
+ echo "$(grep 'NG50' {input.scaffStats} | awk {{'print $4'}})" >> {params.keyValues}
+ echo "$(grep 'N95' {input.scaffStats} | awk {{'print $2'}})" >> {params.keyValues}
+ echo "$(grep 'NG95' {input.scaffStats} | awk {{'print $4'}})" >> {params.keyValues}
+ echo "$(grep 'N100' {input.scaffStats} | awk {{'print $2'}})" >> {params.keyValues}
+ echo "$(grep 'NG100' {input.scaffStats} | awk {{'print $4'}})" >> {params.keyValues}
+ echo "$(grep 'N50' {input.contStats} | awk {{'print $2'}})" >> {params.keyValues}
+ echo "$(grep 'NG50' {input.contStats} | awk {{'print $4'}})" >> {params.keyValues}
+ echo "$(grep 'total_bps' {input.scaffStats} | awk {{'print $3'}})" >> {params.keyValues}
+ echo "$(grep 'sequence_count' {input.scaffStats} | awk {{'print $2'}})" >> {params.keyValues}
+ echo "$(grep 'sequence_count' {input.contStats} | awk {{'print $2'}})" >> {params.keyValues}
+ echo "$(grep 'number_of_gaps' {input.contStats} | awk {{'print $2'}})" >> {params.keyValues}
+ dos2unix {params.keyValues}
+ echo -e "Assembly\nsize_estimate\nmax_heterozygosity\nqv_score\nScaffold_N50_length\nScaffold_NG50_length\nScaffold_N95_length\nScaffold_NG95_length\nScaffold_N100_length\nScaffold_NG100_length\nContig_N50_length\nContig_NG50_length\ntotal_num_bases\ntotal_num_scaffolds\ntotal_num_contigs\nnumber_of_gaps" > {params.rowNames}
+ paste -d'\t' {params.rowNames} {params.keyValues} > {output.keyValuesWithRowNames}
printf "Evaluation complete for {wildcards.sample}, please find these results in {params.resultsPath} folder"
+ rm {params.rowNames} {params.keyValues}
"""
+#
# cp {input.checkLog} {output.merqLog}
#echo "$(grep 'Genome Haploid Length' {input.gscopeSum} | awk {{'print $6'}} | sed 's/,//g')" >> {output.keyValues} put this to remove commas
@@ -433,7 +442,7 @@ rule aggregateAllAssemblies:
"""
cp {input.sampleSheet} {output.newSampleSheet}
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\nScaffold_N50_length\nScaffold_NG50_length\nScaffold_N95_length\nScaffold_NG95_length\nScaffold_N100_length\nScaffold_NG100_length\nContig_N50_length\nContig_NG50_length\ntotal_num_bases\ntotal_num_scaffolds\ntotal_num_contigs\nnumber_of_gaps" | \
paste -d'\t' - {input.allResults} | \
awk -F'\t' '{{s="";for (i=1;i<=NF;i+=2) {{s=s?s FS $i:$i}} print s}}' | \
column -t > {output.results}