No absolute paths

[genomics-kl]

Make paths relative to the workflow directory to avoid issues with special characters in the user's path

[genomics-kl]

GATK (tested v4.6.2.0) seems to have issues with spaces in the path, so the variant calling component of the workflow may not be fixable for this issue.

kin.lau@compute113:test_gatk$ module load bbc2/gatk/gatk-4.6.2.0

gatk --java-options "-Xms8g -Xmx72g -Djava.io.tmpdir=./tmp" \
            MarkDuplicatesSpark \
            --spark-master local[8] \
            -I ../results/star/SRR1039508.Aligned.out.bam \
            -O foo.bam \
            -M foo.metrics \
            --conf spark.executor.cores=8 \
            --conf spark.local.dir=./tmp \
            --conf spark.driver.memory=6g \
            --conf spark.executor.memory=5g

***********************************************************************

A USER ERROR has occurred: Failed to determine total input size of ../results/star/SRR1039508.Aligned.out.bam
 Caused by:File file:/varidata/research/projects/bbc/research/rnaseq_devel%20spaces/results/star/SRR1039508.Aligned.out.bam does not exist

***********************************************************************

kin.lau@compute113:test_gatk$ ls -l "/varidata/research/projects/bbc/research/rnaseq_devel spaces/results/star/SRR1039508.Aligned.out.bam"
-rw-rw----+ 1 kin.lau bbc-modify 8150835 Jul 10 11:33 '/varidata/research/projects/bbc/research/rnaseq_devel spaces/results/star/SRR1039508.Aligned.out.bam'