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Commit ef2d9e9d authored by james94's avatar james94
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new merq naming

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rules/rulesNew.smk
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...@@ -239,8 +239,8 @@ rule merqury: ...@@ -239,8 +239,8 @@ rule merqury:
workflow.cores * 0.5 workflow.cores * 0.5
output: 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.qv"), caption="../report/merqury/qvScore.rst", category="QV Estimate", subcategory="{sample}"),
report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.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}_assembly.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.spectra-cn.fl.png"), caption="../report/merqury/spectra-cn_filled.rst", category="Copy Number Spectra Plots", subcategory="{sample}"), report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.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") os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{sample}" + "_dB.21.hist")
log: log:
os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/logs/{sample}_merqury.log") os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/logs/{sample}_merqury.log")
...@@ -268,8 +268,8 @@ rule merqury: ...@@ -268,8 +268,8 @@ rule merqury:
rule genomescope2: rule genomescope2:
input: 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/" + "{sample}" + "_dB.21.hist"),
check1=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.fl.png"), check1=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.fl.png"),
check2=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.st.png") check2=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.st.png")
params: params:
outFolder=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/"), 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/" + "{sample}" + "_dB.21.histo")
...@@ -347,8 +347,8 @@ rule saveConfiguration_and_getKeyValues: ...@@ -347,8 +347,8 @@ rule saveConfiguration_and_getKeyValues:
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_busco5/short_summary.specific." + buscoDataBaseName + "_odb10." + "{sample}" + ".txt"), busco=os.path.join(config['Results'], "{sample}" + "/1_busco5/short_summary.specific." + buscoDataBaseName + "_odb10." + "{sample}" + ".txt"),
qv=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.qv"), qv=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.qv"),
spectraStacked=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.st.png"), spectraStacked=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.st.png"),
spectraFlat=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.fl.png"), spectraFlat=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.fl.png"),
# os.path.join(config['Results'],"{sample}" + "/QVstats_merylAndMerqury/logs/" + "{sample}" + "_merqury.log"), # os.path.join(config['Results'],"{sample}" + "/QVstats_merylAndMerqury/logs/" + "{sample}" + "_merqury.log"),
# os.path.join(config['Results'],"{sample}" + "/assemblyStats/{sample}_contig_stats.tsv"), # os.path.join(config['Results'],"{sample}" + "/assemblyStats/{sample}_contig_stats.tsv"),
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"),
...@@ -372,8 +372,8 @@ rule saveConfiguration_and_getKeyValues: ...@@ -372,8 +372,8 @@ rule saveConfiguration_and_getKeyValues:
gscopeLin=os.path.join(config['Results'], "{sample}" +"/5_Key_Results/" + "{sample}" + "_gScope_linear_plot.png"), gscopeLin=os.path.join(config['Results'], "{sample}" +"/5_Key_Results/" + "{sample}" + "_gScope_linear_plot.png"),
busco=os.path.join(config['Results'], "{sample}" + "/5_Key_Results/short_summary.specific." + buscoDataBaseName + "_odb10." + "{sample}" + ".txt"), busco=os.path.join(config['Results'], "{sample}" + "/5_Key_Results/short_summary.specific." + buscoDataBaseName + "_odb10." + "{sample}" + ".txt"),
qv=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.qv"), qv=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.qv"),
spectraStacked=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.spectra-cn.st.png"), spectraStacked=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.st.png"),
spectraFlat=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.spectra-cn.fl.png"), spectraFlat=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.fl.png"),
# os.path.join(config['Results'],"{sample}" + "/QVstats_merylAndMerqury/logs/" + "{sample}" + "_merqury.log"), # os.path.join(config['Results'],"{sample}" + "/QVstats_merylAndMerqury/logs/" + "{sample}" + "_merqury.log"),
# os.path.join(config['Results'],"{sample}" + "/assemblyStats/{sample}_contig_stats.tsv"), # os.path.join(config['Results'],"{sample}" + "/assemblyStats/{sample}_contig_stats.tsv"),
scaffStats=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/{sample}_scaffold_stats.tsv"), scaffStats=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/{sample}_scaffold_stats.tsv"),
......
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