slurm, collectInsertSize error, calling Rscript from the path
illumina_qc call the CollectInsertSizeMetrics from picard in the workflows/components/insertssizes.py component. this jar call internally a Rscript command. Rscript is not in the PATH, so the workflow is in error.
"module load system/R-3.4.3" should solve the problem, but we don't manage to exectute it /tools/java/jre1.8.0_45/bin/java -Xmx2g -jar /usr/local/bioinfo/src/picard-tools/picard-2.18.2/picard.jar CollectInsertSizeMetrics HISTOGRAM_WIDTH=800 VALIDATION_STRINGENCY=LENIENT MINIMUM_PCT=0.01 HISTOGRAM_FILE=/work/ng6-test/jflow_mmanno/work/illumina_qc/wf000059/InsertsSizes_default/Demo_NoIndex_L001.pdf INPUT=/work/ng6-test/jflow_mmanno/work/illumina_qc/wf000059/BWA_default/Demo_NoIndex_L001.bam OUTPUT=/work/ng6-test/jflow_mmanno/work/illumina_qc/wf000059/InsertsSizes_default/Demo_NoIndex_L001.txt 2> /work/ng6-test/jflow_mmanno/work/illumina_qc/wf000059/InsertsSizes_default/Demo_NoIndex_L001.log