tb_profiler WDL Basic WDLization of TBProfiler. Features both bam-as-input mode and fastq-as-input mode. Extracts strain, drug resistance status, and median coverage into separate report files. The Docker image is based upon staphb/tbprofiler but uses a reference genome with a different chromosome name. It's the same NC_000962.3 you know and love. Notes Use --copy-input-files if using miniwdl For the bam version of the pipeline, "_to_Ref.H37Rv.bam" will be removed from the bam's filename to generate the sample name unless bam_suffix is set For the fastq version of the pipeline, everything after the first underscore of the first fastq's filename will be removed to generate the sample name When using the bam version of the pipeline, your bam MUST be aligned to the same reference genome as the one in this repo! Samples that return no lineage, like SAMN0657912, will return an empty string for strain A comparison of the same sample at different points in myco_sra TBProfiler can be found in examples/results_from_bam and examples/results_from_fastq