Fix R scripts (#16)

* chmod +x * add correct path to Rscript * update CHANGELOG
nf-core · Jun 24, 2019 · 10eff4e · 10eff4e
1 parent 89cac8b
commit 10eff4e
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -52,6 +52,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 -   [#12](https://github.com/nf-core/sarek/pull/12) - Simplify `check_max()` function
 -   [#13](https://github.com/nf-core/sarek/pull/13) - Merge `BamQCmapped` and `BamQCrecalibrated` processes into `BamQC` process
 -   [#13](https://github.com/nf-core/sarek/pull/13) - Split `CompressVCF` process into `CompressVCFsnpEff` and `CompressVCFvep` processes
+-   [#16](https://github.com/nf-core/sarek/pull/16) - Make scripts in `bin/` and `scripts/` executable
 
 ### `Removed`
 
@@ -63,6 +64,8 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 -   [#3](https://github.com/nf-core/sarek/pull/3) - Fix Docker ownership
 -   [#11](https://github.com/nf-core/sarek/pull/11) - Fix MergeMpileup PublishDir
 -   [#13](https://github.com/nf-core/sarek/pull/13) - Fix merge in annotation
+-   [#14](https://github.com/nf-core/sarek/pull/14) - Fix output name for vcf files
+-   [#16](https://github.com/nf-core/sarek/pull/16) - Fix path to Rscript
 
 ## [2.3.FIX1] - 2019-03-04
 

diff --git a/bin/convertAlleleCounts.r b/bin/convertAlleleCounts.r
diff --git a/bin/run_ascat.r b/bin/run_ascat.r
diff --git a/main.nf b/main.nf
@@ -1359,7 +1359,7 @@ process ConvertAlleleCounts {
     script:
     gender = genderMap[idPatient]
     """
-    convertAlleleCounts.r ${idSampleTumor} ${alleleCountTumor} ${idSampleNormal} ${alleleCountNormal} ${gender}
+    Rscript ${workflow.projectDir}/bin/convertAlleleCounts.r ${idSampleTumor} ${alleleCountTumor} ${idSampleNormal} ${alleleCountNormal} ${gender}
     """
 }
 
@@ -1387,7 +1387,7 @@ process Ascat {
     """
     # get rid of "chr" string if there is any
     for f in *BAF *LogR; do sed 's/chr//g' \$f > tmpFile; mv tmpFile \$f;done
-    run_ascat.r ${bafTumor} ${logrTumor} ${bafNormal} ${logrNormal} ${idSampleTumor} ${baseDir} ${acLociGC}
+    Rscript ${workflow.projectDir}/bin/run_ascat.r ${bafTumor} ${logrTumor} ${bafNormal} ${logrNormal} ${idSampleTumor} ${baseDir} ${acLociGC}
     """
 }
 

diff --git a/scripts/ascat.R b/scripts/ascat.R
diff --git a/scripts/filter_locifile.py b/scripts/filter_locifile.py
diff --git a/scripts/selectROI.py b/scripts/selectROI.py