I encountered an issue when using strelka VCF files where the GT is missing from the FORMAT field for the NORMAL and TUMOR samples. This may be outside of the scope of the strelka docker container, but it could be added to the helper script as well. This was working in a standalone workflow:

awk '{if(/^##/) print; else if(/^#/) print "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n"$0; else print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\tGT:"$9"\t./.:"$10"\t./.:"$11;}' $OUTPUT_DIR/results/all.somatic.snvs.vcf > $OUTPUT_DIR/results/all.somatic.snvs.gt.vcf awk '{if(/^##/) print; else if(/^#/) print "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n"$0; else print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\tGT:"$9"\t./.:"$10"\t./.:"$11;}' $OUTPUT_DIR/results/all.somatic.indels.vcf > $OUTPUT_DIR/results/all.somatic.indels.gt.vcf

The same could be done with the passed VCF files as well:

awk '{if(/^##/) print; else if(/^#/) print "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n"$0; else print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\tGT:"$9"\t./.:"$10"\t./.:"$11;}' $OUTPUT_DIR/results/passed.somatic.snvs.vcf > $OUTPUT_DIR/results/passed.somatic.snvs.gt.vcf awk '{if(/^##/) print; else if(/^#/) print "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n"$0; else print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\tGT:"$9"\t./.:"$10"\t./.:"$11;}' $OUTPUT_DIR/results/passed.somatic.indels.vcf > $OUTPUT_DIR/results/passed.somatic.indels.gt.vcf