build rmd to md documentation

bamboo/build.sh

@@ -72,9 +72,9 @@ sshpass -f $SVC_PASS ssh $SVC_USER@$BUILD_SERVER "cd $(dirname $TEMP_DIR); scp -
 # sshpass -f $SVC_PASS scp -r * $SVC_USER@$BUILD_SERVER:$TEMP_DIR
 
 echo "schedule the build remotely"
-# sshpass -f $SVC_PASS ssh $SVC_USER@$BUILD_SERVER "$TEMP_DIR/bamboo/pbs_remote.sh $TEMP_DIR/bamboo/build.pbs $TEMP_DIR"
 WORK_DIR="$ASSOC_DIR/nextflow_temp/$PLAN_NAME"
 sshpass -f $SVC_PASS ssh $SVC_USER@$BUILD_SERVER "TEMP_DIR=$TEMP_DIR IMAGE_CACHE=$IMAGE_CACHE WORK_DIR=$WORK_DIR $TEMP_DIR/bamboo/build_pipeline.sh"
+sshpass -f $SVC_PASS ssh $SVC_USER@$BUILD_SERVER "$TEMP_DIR/bamboo/pbs_remote.sh $TEMP_DIR/bamboo/build_documentation.pbs $TEMP_DIR"
 echo "remote job scheduled"
 wait # wait for pbs jobs to finish running
 

bamboo/build_documentation.pbs

@@ -0,0 +1,28 @@
+#!/bin/bash
+#PBS -N cutandrun_docs
+#PBS -q paidq
+#PBS -P 95b3beda-8f4a-41a6-ac94-0aaad86bfd9d
+#PBS -M [email protected]
+#PBS -l select=1:mem=16gb:ncpus=1
+#PBS -j oe
+#PBS -m a
+#PBS -o /active/taylor_s/build/RPDEV/cutandrun_nf/logs
+
+set -eou pipefail
+
+# Set-up Environment, load R
+export RSTUDIO_PANDOC="/usr/lib/rstudio-server/bin/pandoc"
+module load R/4.1.0-foss-2020b
+
+# change directory to temp dir
+cd $TEMP_DIR
+
+# create artifacts directory
+echo "create artifact dir"
+mkdir -p artifacts
+
+# render the markdown file
+Rscript -e 'rmarkdown::render("workflow_docs/run_workflow.Rmd", encoding = "UTF-8")'
+
+# copy output to artifacts dir
+cp -r workflow_docs artifacts/

workflow_docs/run_workflow.md

@@ -438,7 +438,7 @@ Edit the script `main_run.sh` and change the values for the
 `NFX_PROFILE` variable if desired.
 
     ## #Options: 'PBS_apptainer','local_apptainer','local_singularity', 'PBS_singularity'
-    ## NFX_PROFILE='PBS_apptainer'
+    ## NFX_PROFILE='PBS_singularity'
 
 ## Alignment and Peak Calls