add bbmap.BBMapTool().dedup_clumpify(), along with unit tests

pass JVMmemory to bbmap and clumpify; add rmdup_clumpify_bam to read_utils.py; change TestRmdupUnaligned unit tests for bbmap to use read_utils.py::rmdup_clumpify_bam; add dedup_bam WDL task to tasks_read_utils.wdl

replace mvicuna-based read deduplication in taxon_filter.py::deplete() with clumpify-based deduplication that occurs farther upstream in advance of BWA-based depletion; add dedup_bam WDL workflow; in dedup_bam WDL task, create and emit FastQC report of only de-duplicated reads; update unit test input to include dup reads, and update expected output for the test_taxon_filter::TestDepleteHuman integration tests to reflect difference in output from clumpify vs previous mvicuna output

DNAnexus seems to have replaced their wiki with a new documentation page ( https://documentation.dnanexus.com/downloads ) and the old download URLs along with it

Allow containments (where one sequence is shorter) when using bbmap clumpify to deduplicate

…al-ngs into ct-add-clumpify

…on raw rather than de-duped reads

fix bug in conda command quiet calling ('-q -y' must be after 'conda <command>')

for bbmap clumpify de-dup, merge like-library RGs and perform deduplication on each, then gather the IDs of kept reads, and filter the input sam based on the list of IDs to keep so as to maintain header and RG information. move most of the theprocessing to bbmap.py::dedup_clumpify so it has a more simple interface that accepts one bam and emits one bam. ToDo: parallelize across LBs

…kflow

change to clumpify for pre-depletion dedup; dedup lication can be likely be removed from depletion entirely in the future once all calls in the codebase have been updated to have one fewer arg

remove rmdup from depletion call, remove *.rmdup.bam from positional arguments for depletion CLI parser, remove *.rmdup.bam from inputs where depletion is called (test cases, WDL), remove *.rmdup.bam from expected depletion outputs. Chance Snakemake merge_one_per_sample rule to call  rmdup_clumpify_bam rather than rmdup_mvicuna_bam

single-end reads do not have /1 /2 mate suffix, so pass through IDs missing the suffix