Reduce memory footprint for STAR (resolves #97)

Reduced from 2 * reference_size to 1.85 * reference_size so the requirement for a full run will be < 50G

src/protect/alignment/rna.py

@@ -35,7 +35,7 @@ def align_rna(job, fastqs, univ_options, star_options):
     """
     star = job.wrapJobFn(run_star, fastqs, univ_options, star_options,
                          cores=star_options['n'],
-                         memory=PromisedRequirement(lambda x: 2 * x.size,
+                         memory=PromisedRequirement(lambda x: 1.85 * x.size,
                                                     star_options['tool_index']),
                          disk=PromisedRequirement(star_disk, fastqs, star_options['tool_index']))
     index = job.wrapJobFn(index_star, star.rv(), univ_options,

src/protect/pipeline/ProTECT.py

@@ -30,11 +30,11 @@
 from math import ceil
 
 from protect.addons import run_mhc_gene_assessment
-from protect.alignment.dna import align_dna, bwa_disk
-from protect.alignment.rna import align_rna, star_disk
+from protect.alignment.dna import align_dna
+from protect.alignment.rna import align_rna
 from protect.binding_prediction.common import spawn_antigen_predictors, merge_mhc_peptide_calls
 from protect.common import delete_fastqs, ParameterError
-from protect.expression_profiling.rsem import rsem_disk, wrap_rsem
+from protect.expression_profiling.rsem import wrap_rsem
 from protect.haplotyping.phlat import merge_phlat_calls, phlat_disk, run_phlat
 from protect.mutation_annotation.snpeff import run_snpeff, snpeff_disk
 from protect.mutation_calling.common import run_mutation_aggregator