Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

fix Ascat R script execution #127

Merged
merged 15 commits into from
Feb 25, 2020
Merged

fix Ascat R script execution #127

Show file tree
Hide file tree
Changes from 6 commits
Commits
Show all changes
15 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion bin/convertAlleleCounts.r
View file
Open in desktop
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.
#
Expand Down
2 changes: 1 addition & 1 deletion bin/run_ascat.r
View file
Open in desktop
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
4 changes: 2 additions & 2 deletions conf/igenomes.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ params {
genomes {
'GRCh37' {
ac_loci = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci"
ac_lociGC = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci.gc"
ac_loci_gc = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci.gc"
bwa = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.{amb,ann,bwt,pac,sa}"
chr_dir = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/Chromosomes"
chr_length = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/Length/human_g1k_v37_decoy.len"
Expand All @@ -31,7 +31,7 @@ params {
}
'GRCh38' {
ac_loci = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci"
ac_lociGC = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci.gc"
ac_loci_gc = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci.gc"
bwa = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/Homo_sapiens_assembly38.fasta.64.{alt,amb,ann,bwt,pac,sa}"
chr_dir = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes"
chr_length = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len"
Expand Down
17 changes: 5 additions & 12 deletions main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
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 @@ -2597,18 +2597,11 @@ process Ascat {
gender = genderMap[idPatient]
ascat_purity=params.ascat_purity
ascat_ploidy=params.ascat_ploidy
if (params.ascat_purity && params.ascat_ploidy)
purity_ploidy = (params.ascat_purity && params.ascat_ploidy) ? "--purity ${params.ascat_purity} --ploidy ${params.ascat_ploidy}" : ""
ggabernet marked this conversation as resolved.
Show resolved Hide resolved
"""
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}
"""
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}
"""


for f in *BAF *LogR; do sed 's/chr//g' \$f > tmpFile; mv tmpFile \$f;done
run_ascat.r --tumorbaf ${bafTumor} --tumorlogr ${logrTumor} --normalbaf ${bafNormal} --normallogr ${logrNormal} --tumorname ${idSampleTumor} --basedir ${baseDir} --gcfile ${acLociGC} --gender ${gender} ${purity_ploidy}
"""""
}

ascatOut.dump(tag:'ASCAT')
Expand Down