Tidy up and add mock optional file example

Dockerfile

@@ -1,8 +1,8 @@
 ARG BASEIMAGE=ontresearch/base-workflow-image:v0.1.0
 FROM $BASEIMAGE
+ARG ENVFILE=environment.yaml
 
-# Minimal install for example purposes
+COPY $ENVFILE $HOME/environment.yaml
-COPY environment.yaml $HOME/environment.yaml 
 RUN \
     . $CONDA_DIR/etc/profile.d/mamba.sh \
     && micromamba activate \

data/OPTIONAL_FILE

@@ -0,0 +1,11 @@
+# Nothing to see here. A sentinel file to replace real data.
+# e.g.:
+#
+# input:
+#     file some_data
+#     file extra_data
+# script:
+# def extra = extra_data.name != 'OPTIONAL_FILE' ? "--extra-data $opt" : ''
+# """
+# command ${some_data} ${extra}
+# """

nextflow.config

@@ -65,7 +65,6 @@ profiles {
     awsbatch {
         process {
             executor = 'awsbatch'
-            //queue = "${params.aws_queue}"
             queue = "${params.aws_queue}"
             memory = '8G'
             withLabel:pysam {