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