Rr wdl 20210219

Metaflye pipeline wdl. Works given an appropriate inputs.json e.g.

{ "metaflye.input_fastq" : [ "/global/dna/dm_archive/rqc/analyses/AUTO-308887/pbio-2337.21509.ccs.filter.fastq.gz", "/global/dna/dm_archive/rqc/analyses/AUTO-310142/pbio-2341.21539.ccs.filter.fastq.gz" ], "metaflye.flye_container" : "quay.io/biocontainers/flye:2.8.1--py37h4bd9754_0", "metaflye.flye_parameters" : "--meta -t 32 --out-dir flye --pacbio-hifi", "metaflye.smrtlink_container" : "bryce911/smrtlink:8.0.0.80529", "metaflye.input_bam" : [ "/global/dna/dm_archive/rqc/analyses/AUTO-308895/pbio-2337.21509.filter.subreads.bam", "/global/dna/dm_archive/rqc/analyses/AUTO-310147/pbio-2341.21539.filter.subreads.bam" ], "metaflye.minimap2_container" : "quay.io/biocontainers/minimap2:2.17--h8b12597_1", "metaflye.samtools_container" : "quay.io/biocontainers/samtools:1.9--h8571acd_11", "metaflye.bbtools_container" : "bryce911/bbtools:38.79" }