pipeline.mro

@include "stages.mro"
filetype csv;
filetype bam;
filetype vcf;
filetype vcf.gz;
filetype bed;

pipeline VARIANT_CALL_CB_CLUSTERS(
    in bam possorted_bam,
    in csv barcode_clusters,
    in string reference_path,
    out vcf.gz variants,
    out bam[] merged_bams,
)
{
    call FILTER_BAM(
        possorted_bam = self.possorted_bam,
        barcode_clusters = self.barcode_clusters,
    )
    call MODIFY_BAM(
        filtered_bams = FILTER_BAM.filtered_bams,
        reference_path = self.reference_path,
    )
    call MERGE_BAMS(
        modified_filtered_bams = MODIFY_BAM.modified_filtered_bams,
        clusters = FILTER_BAM.clusters,
    )
    call CALL_VARIANTS(
        merged_bams = MERGE_BAMS.merged_bams,
        merged_clusters = MERGE_BAMS.merged_clusters,
        reference_path = self.reference_path,
    )
    return (
        variants = CALL_VARIANTS.variants,
        merged_bams = MERGE_BAMS.merged_bams,
    )
}