Merge pull request #937 from mskcc/bugfix/oncokb_authentication

hotfix/1.4.3

conf/containers.config

@@ -46,7 +46,7 @@
     container = "cmopipeline/bcftools-vt:1.2.3"
   }
   withName:SomaticAnnotateMaf {
-    container = "cmopipeline/vcf2maf:vep88_1.2.5"
+    container = "cmopipeline/vcf2maf:vep88_1.2.7"
   }
   withName:DoFacets {
     container = "cmopipeline/facets-suite-preview-htstools:0.0.1"
@@ -98,7 +98,7 @@
     container = "cmopipeline/bcftools-vt:1.2.2"
   }
   withName:GermlineAnnotateMaf {
-    container = "cmopipeline/vcf2maf:vep88_1.2.5"
+    container = "cmopipeline/vcf2maf:vep88_1.2.7"
   }
   withName:GermlineFacetsAnnotation {
     container = "cmopipeline/facets-suite-preview-htstools:0.0.1"

containers/vcf2maf/Dockerfile

@@ -4,7 +4,7 @@ LABEL maintainer="Christopher Allan Bolipata ([email protected])" \
       contributor="Nikhil Kumar ([email protected])" \
       contributor="Philip Jonsson ([email protected])" \
       contributor="Anne Marie Noronha ([email protected])" \
-      version.image="1.2.5" \
+      version.image="1.2.7" \
       version.vcf2maf="1.6.17" \
       version.vep="88" \
       version.htslib="1.9" \
@@ -15,7 +15,7 @@ LABEL maintainer="Christopher Allan Bolipata ([email protected])" \
       version.oncokb_annotator="1.1.0" \
       version.filter_somatic_maf="0.6.2" \
       version.filter_germline_maf="0.2.2" \
-      version.annotateMaf="1.0.1" \
+      version.annotateMaf="1.0.2" \
       source.vcf2maf="https://github.com/mskcc/vcf2maf/releases/tag/v1.6.17" \
       source.vep="http://dec2016.archive.ensembl.org/info/docs/tools/vep/script/vep_download.html#versions" \
       source.htslib="https://github.com/samtools/htslib/releases/tag/1.9" \
@@ -30,7 +30,7 @@ ENV HTSLIB_VERSION 1.9
 ENV SAMTOOLS_VERSION 1.9
 ENV BCFTOOLS_VERSION 1.9
 ENV ONCOKB_VERSION 1.1.0
-ENV ANNOTATE_MAF 1.0.1
+ENV ANNOTATE_MAF 1.0.2
 
 RUN apt-get update --fix-missing && apt-get install -y \
     tcsh \

pipeline.nf

@@ -699,7 +699,7 @@ if (params.pairing) {
 
   // Parse input FASTQ mapping
 
-  inputPairing.into{pairing4T; pairing4N; pairingTN; pairing4QC; inputPairing}
+  inputPairing.into{pairing4T; pairing4N; pairingTN; pairing4QC; inputPairing; pairing4Qualimap}
   bamsBQSR4Tumor.combine(pairing4T)
                           .filter { item ->
                             def idSample = item[0]
@@ -1472,6 +1472,7 @@ process SomaticAnnotateMaf {
     --filter-vcf 0
     
   python /usr/bin/oncokb_annotator/MafAnnotator.py \
+    -u "https://legacy.oncokb.org/api/v1" \
     -i ${outputPrefix}.raw.maf \
     -o ${outputPrefix}.raw.oncokb.maf
 
@@ -2561,7 +2562,7 @@ process QcQualimap {
     set idSample, target, file(bam), file(bai), file(targetsBed) from bamsBQSR4Qualimap
 
   output:
-    set idSample, file("${idSample}_qualimap_rawdata.tar.gz") into qualimap4MultiQC, qualimap4Tumor, qualimap4Normal, qualimap4Aggregate
+    set idSample, file("${idSample}_qualimap_rawdata.tar.gz") into qualimap4MultiQC, qualimap4MultiQC2, qualimap4Aggregate
     set idSample, file("*.html"), file("css/*"), file("images_qualimapReport/*") into qualimapOutput
 
   when: runQC   
@@ -2606,10 +2607,19 @@ process QcQualimap {
   """
 }
 
-qualimap4Tumor.combine(qualimap4Normal)
-  .map{ idTumor,  qualimapTumor, idNormal, qualimapNormal ->
-    [idTumor, idNormal, qualimapTumor, qualimapNormal]
-  }.set{qualimap4Pairing}
+pairing4Qualimap
+  .combine(qualimap4MultiQC2)
+  .branch{ idTumor, idNormal, idSample, qualimapDir ->
+    tumor:  idSample == idTumor
+    normal: idSample == idNormal
+  }
+  .set{qualimap4PairedTN}
+
+qualimap4PairedTN.tumor.combine(qualimap4PairedTN.normal, by:[0,1])
+  .view()
+  .map{ idTumor,idNormal, idSample1, qualimapDir1, idSample2, qualimapDir2 ->
+    [idTumor,idNormal,qualimapDir1,qualimapDir2]
+  }.set{qualimap4SomaticMultiQC}
 
 Channel.from(true, false).set{ ignore_read_groups }
 bamsBQSR4Alfred
@@ -2873,7 +2883,7 @@ process QcConpair {
 
 conpairOutput
   .map{ placeholder, idTumor, idNormal, conpairFiles -> [idTumor, idNormal, conpairFiles] }
-  .join(qualimap4Pairing, by:[0,1]) 
+  .join(qualimap4SomaticMultiQC, by:[0,1]) 
   .join(FacetsQC4SomaticMultiQC, by:[0,1]) // idTumor, idNormal, conpairFiles, qualimapTumor, qualimapNormal, facetsSummaryFiles, facetsQcFiles 
   .set{somaticMultiQCinput}