Apply fixes, linting

Author: scwatts

modules/local/peach/Dockerfile

@@ -12,12 +12,12 @@ channels:\n\
     - defaults'
 
 RUN \
-  conda create -y -p /env/ \
-    'openjdk >=8'
+    conda create -y -p /env/ \
+        'openjdk >=8'
 
 RUN \
-  mkdir -p /opt/peach/ && \
-  wget -O /opt/peach/peach.jar 'https://github.com/hartwigmedical/hmftools/releases/download/peach-v2.0.0/peach_v2.0.0.jar'
+    mkdir -p /opt/peach/ && \
+    wget -O /opt/peach/peach.jar 'https://github.com/hartwigmedical/hmftools/releases/download/peach-v2.0.0/peach_v2.0.0.jar'
 
 RUN \
     conda clean -yaf

modules/local/peach/main.nf

@@ -42,11 +42,11 @@ process PEACH {
     """
     mkdir -p peach/
 
-    touch peach/${meta.tumor_id}.peach.events.tsv
-    touch peach/${meta.tumor_id}.peach.gene.events.tsv
-    touch peach/${meta.tumor_id}.peach.haplotypes.all.tsv
-    touch peach/${meta.tumor_id}.peach.haplotypes.best.tsv
-    touch peach/${meta.tumor_id}.peach.qc.tsv
+    touch peach/${meta.sample_id}.peach.events.tsv
+    touch peach/${meta.sample_id}.peach.gene.events.tsv
+    touch peach/${meta.sample_id}.peach.haplotypes.all.tsv
+    touch peach/${meta.sample_id}.peach.haplotypes.best.tsv
+    touch peach/${meta.sample_id}.peach.qc.tsv
 
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """

subworkflows/local/peach_calling/main.nf

@@ -34,7 +34,10 @@ workflow PEACH_CALLING {
             ]
         }
         .branch { meta, purple_dir ->
-            runnable: purple_dir
+
+            def has_normal = Utils.hasNormalDna(meta)
+
+            runnable: purple_dir && has_normal
             skip: true
                 return meta
         }