Fail if empty ref_alt ?

Hi,

The alignment task is taken to a failed state if there are no ALT contigs (ref_alt file has no content). Why is this?

In the command ref_alt is not used but there's an if statement requiring this:

    # if ref_alt has data in it,
    if [ -s ${ref_alt} ]; then
      java -Xms5000m -jar /usr/gitc/picard.jar \
        SamToFastq \
        INPUT=${input_bam} \
        FASTQ=/dev/stdout \
        INTERLEAVE=true \
        NON_PF=true | \
      /usr/gitc/${bwa_commandline} /dev/stdin - 2> >(tee ${output_bam_basename}.bwa.stderr.log >&2) | \
      java -Dsamjdk.compression_level=${compression_level} -Xms3000m -jar /usr/gitc/picard.jar \
        MergeBamAlignment \
        VALIDATION_STRINGENCY=SILENT \
        EXPECTED_ORIENTATIONS=FR \
        ATTRIBUTES_TO_RETAIN=X0 \
        ATTRIBUTES_TO_REMOVE=NM \
        ATTRIBUTES_TO_REMOVE=MD \
        ALIGNED_BAM=/dev/stdin \
        UNMAPPED_BAM=${input_bam} \
        OUTPUT=${output_bam_basename}.bam \
        REFERENCE_SEQUENCE=${ref_fasta} \
        PAIRED_RUN=true \
        SORT_ORDER="unsorted" \
        IS_BISULFITE_SEQUENCE=false \
        ALIGNED_READS_ONLY=false \
        CLIP_ADAPTERS=false \
        MAX_RECORDS_IN_RAM=2000000 \
        ADD_MATE_CIGAR=true \
        MAX_INSERTIONS_OR_DELETIONS=-1 \
        PRIMARY_ALIGNMENT_STRATEGY=MostDistant \
        PROGRAM_RECORD_ID="bwamem" \
        PROGRAM_GROUP_VERSION="${bwa_version}" \
        PROGRAM_GROUP_COMMAND_LINE="${bwa_commandline}" \
        PROGRAM_GROUP_NAME="bwamem" \
        UNMAPPED_READ_STRATEGY=COPY_TO_TAG \
        ALIGNER_PROPER_PAIR_FLAGS=true \
        UNMAP_CONTAMINANT_READS=true \
        ADD_PG_TAG_TO_READS=false

      grep -m1 "read .* ALT contigs" ${output_bam_basename}.bwa.stderr.log | \
      grep -v "read 0 ALT contigs"

    # else ref_alt is empty or could not be found
    else
      exit 1;
    fi

https://github.com/gatk-workflows/five-dollar-genome-analysis-pipeline/blob/3ad22df4bfaa605b6a5504f110264b2b08100128/tasks_pipelines/alignment.wdl#L71

The reason I'm asking is that I'd like to run this with hg19 / b37 reference data.

Thanks! Juho

gatk-workflows / five-dollar-genome-analysis-pipeline

Fail if empty ref_alt ? #11