Commit ad4c1c77 authored by Eric CHARPENTIER's avatar Eric CHARPENTIER 🐍
Browse files

fixed creation of clustDE output and input when no DEG found 2 - thx atorres

parent 441d694b
......@@ -274,7 +274,7 @@ rule deseq2:
rule deg:
input: rdata=OUTPUTDIR+"/DESEQ2/rData/dds.RData"
output: expand(OUTPUTDIR+"/DESEQ2/results/{{comp}}/{{comp}}_{file}",file=["DEseqRes.tsv","All_DEG.tsv","UP_DEG.tsv","DOWN_DEG.tsv","Volcano-plot.png","MA-plot.png","clustDEgene.png","clustDEgene.pdf"])
output: expand(OUTPUTDIR+"/DESEQ2/results/{{comp}}/{{comp}}_{file}",file=["DEseqRes.tsv","All_DEG.tsv","UP_DEG.tsv","DOWN_DEG.tsv","Volcano-plot.png","MA-plot.png","clustDEgene.png"])
params: cond1=lambda wildcards : getConditionForComp(wildcards)["cond1"],
cond2=lambda wildcards : getConditionForComp(wildcards)["cond2"]
shell: """
......@@ -286,7 +286,7 @@ rule annot:
input: expand(OUTPUTDIR+"/DESEQ2/results/{{comp}}/{{comp}}_{file}", file=["All_DEG.tsv","DEseqRes.tsv"]),
corrAnnotations=(SCRIPTPATH+"/corresIDorg.txt"),
rdata=OUTPUTDIR+"/DESEQ2/rData/dds.RData"
output: expand(OUTPUTDIR+"/DESEQ2/results/{{comp}}/{{comp}}_{file}",file=["dotplotGO.png","annotGo.tsv","dotplotKEGG.png","annotKegg.tsv","gseGo.txt","gseKegg.txt"])
output: expand(OUTPUTDIR+"/DESEQ2/results/{{comp}}/{{comp}}_{file}",file=["gseGo.txt","gseKegg.txt"])
params: cond1=lambda wildcards : getConditionForComp(wildcards)["cond1"],
cond2=lambda wildcards : getConditionForComp(wildcards)["cond2"]
shell: """
......@@ -297,7 +297,7 @@ rule annot:
rule copyDataForReport:
input:
expand(OUTPUTDIR+"/DESEQ2/results/{suffixe}",suffixe=["NormalizedCountMatrix.txt","NormalizedCountMatrixFiltered.txt","PCAplot.png","sampletosampledistance.jpeg"]),
expand(OUTPUTDIR+"/DESEQ2/results/{comp}/{comp}_{file}",file=["dotplotGO.png","annotGo.tsv","dotplotKEGG.png","annotKegg.tsv","gseGo.txt","gseKegg.txt","DEseqRes.tsv","All_DEG.tsv","UP_DEG.tsv","DOWN_DEG.tsv","Volcano-plot.png","MA-plot.png","clustDEgene.png","clustDEgene.pdf"], comp=COMPARISONS)
expand(OUTPUTDIR+"/DESEQ2/results/{comp}/{comp}_{file}",file=["gseGo.txt","gseKegg.txt","DEseqRes.tsv","All_DEG.tsv","UP_DEG.tsv","DOWN_DEG.tsv","Volcano-plot.png","MA-plot.png","clustDEgene.png"], comp=COMPARISONS)
output:
temp(touch(OUTPUTDIR+"/Report/TEMPLATE/templateCopied.txt"))
params:
......
#$ -s /bin/bash
#$ -cwd
#$ -V
......
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