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fix Ascat R script execution #127

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Merged
maxulysse merged 15 commits into from
Feb 25, 2020
Merged

fix Ascat R script execution #127

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789125e
fix ascat R script execution
ggabernet Feb 24, 2020
42fa68b
Merge branch 'dev' into dev
ggabernet Feb 24, 2020
0794202
skip gc correction
ggabernet Feb 24, 2020
d1e9846
fix ac_loci_gc input
ggabernet Feb 25, 2020
5b0aa1d
improve process ascat Maxime suggestion
ggabernet Feb 25, 2020
157d341
trim empty lines
ggabernet Feb 25, 2020
b2ec3d7
Revert "fix ac_loci_gc input"
ggabernet Feb 25, 2020
9ea0084
Merge branch 'dev' into dev
ggabernet Feb 25, 2020
84149af
add ascat to test
ggabernet Feb 25, 2020
804fa46
Merge branch 'dev' of github.com:ggabernet/sarek into dev
ggabernet Feb 25, 2020
188fc10
remove ascat test
ggabernet Feb 25, 2020
9bba200
Update bin/run_ascat.r
ggabernet Feb 25, 2020
9a551c1
fix ascat process
ggabernet Feb 25, 2020
ba00eb1
Merge branch 'dev' of github.com:ggabernet/sarek into dev
ggabernet Feb 25, 2020
1b088c0
fix trailing spaces
ggabernet Feb 25, 2020
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3 changes: 2 additions & 1 deletion bin/convertAlleleCounts.r
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
#!/bin/env Rscript
#!/usr/bin/env Rscript

# Description:
# R-script for converting output from AlleleCount to BAF and LogR values.
#
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4 changes: 2 additions & 2 deletions bin/run_ascat.r
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
q#!/bin/env Rscript
#!/usr/bin/env Rscript
library("optparse")
option_list = list(
make_option("--tumorbaf", type="character", default=NULL,
Expand Down Expand Up @@ -52,7 +52,7 @@ if(opt$gender=="XY"){


#GC wave correction
ascat.bc = ascat.GCcorrect(ascat.bc, opt$gcfile)
#ascat.bc = ascat.GCcorrect(ascat.bc, opt$gcfile)

#Plot the raw data
ascat.plotRawData(ascat.bc)
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6 changes: 3 additions & 3 deletions main.nf
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Expand Up @@ -2569,7 +2569,7 @@ process ConvertAlleleCounts {
script:
gender = genderMap[idPatient]
"""
Rscript ${workflow.projectDir}/bin/convertAlleleCounts.r ${idSampleTumor} ${alleleCountTumor} ${idSampleNormal} ${alleleCountNormal} ${gender}
convertAlleleCounts.r ${idSampleTumor} ${alleleCountTumor} ${idSampleNormal} ${alleleCountNormal} ${gender}
"""
}

Expand Down Expand Up @@ -2600,12 +2600,12 @@ process Ascat {
if (params.ascat_purity && params.ascat_ploidy)
"""
for f in *BAF *LogR; do sed 's/chr//g' \$f > tmpFile; mv tmpFile \$f;done
Rscript ${workflow.projectDir}/bin/run_ascat.r --tumorbaf ${bafTumor} --tumorlogr ${logrTumor} --normalbaf ${bafNormal} --normallogr ${logrNormal} --tumorname ${idSampleTumor} --basedir ${baseDir} --gcfile ${acLociGC} --gender ${gender} --purity ${ascat_purity} --ploidy ${ascat_ploidy}
run_ascat.r --tumorbaf ${bafTumor} --tumorlogr ${logrTumor} --normalbaf ${bafNormal} --normallogr ${logrNormal} --tumorname ${idSampleTumor} --basedir ${baseDir} --gcfile ${acLociGC} --gender ${gender} --purity ${ascat_purity} --ploidy ${ascat_ploidy}
"""
else
"""
for f in *BAF *LogR; do sed 's/chr//g' \$f > tmpFile; mv tmpFile \$f;done
Rscript ${workflow.projectDir}/bin/run_ascat.r --tumorbaf ${bafTumor} --tumorlogr ${logrTumor} --normalbaf ${bafNormal} --normallogr ${logrNormal} --tumorname ${idSampleTumor} --basedir ${baseDir} --gcfile ${acLociGC} --gender ${gender}
run_ascat.r --tumorbaf ${bafTumor} --tumorlogr ${logrTumor} --normalbaf ${bafNormal} --normallogr ${logrNormal} --tumorname ${idSampleTumor} --basedir ${baseDir} --gcfile ${acLociGC} --gender ${gender}
"""


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