Update pipeline_details.md

doc/pipeline_details.md

@@ -78,13 +78,13 @@ The genMapIndex process generates the GenMap [7] index for the reference sequenc
 The genMapMap process calculates the mappability for the reference sequence using GenMap (`genmap map -K 30 -E 2 -b`). It then filters the GenMap results using [`filterGM.rb`](ruby_r_scripts.md#filterGMrb) to exclude any sequences with mappability < 1.0 (`filterGM.rb <raw_genmap.bed> 1.0 exclude > <genmap.1.0.bed>`).  
 
 ## repeatMask  
-The repeatMask process uses RepeatMasker [8] to soft-mask repeat regions in the reference sequence based on a pre-defined target species (`RepeatMasker -gccalc -nolow -species <specified species>`). The soft-masked reference sequence is passed to the repeatModeler process.  
+The repeatMask process uses RepeatMasker [8] to soft-mask repeat regions in the reference sequence based on a pre-defined target species (`RepeatMasker -gccalc -nolow -xsmall -species <specified species>`). The soft-masked reference sequence is passed to the repeatModeler process.  
 
 ## repeatModeler  
 The repeatModeler process uses RepeatModeler [9] and the RepeatMasker soft-masked reference sequence to generate a species-specific repeat library for the reference sequence. First, a database is built using `BuildDatabase`, then the library is built using `RepeatModeler`. The resulting library (`consensi.fa.classified`) RepeatMasker -pa ${rm_pa} -gccalc -nolow -lib consensi.fa.classified is passed to the repeatMaskRM process.  
 
 ## repeatMaskRM  
-The repeatMaskRM process uses RepeatMasker and the RepeatModeler custom repeat library to soft mask the reference sequence (`RepeatMasker -gccalc -nolow -lib consensi.fa.classified`). The RepeatMasker out file (.out) is then converted to bed using [`RM2bed.rb`](ruby_r_scripts.md#RM2bedrb).  
+The repeatMaskRM process uses RepeatMasker and the RepeatModeler custom repeat library to soft mask the reference sequence (`RepeatMasker -gccalc -nolow -xsmall -lib consensi.fa.classified`). The RepeatMasker out file (.out) is then converted to bed using [`RM2bed.rb`](ruby_r_scripts.md#RM2bedrb).  
 
 ## maskIndels  
 Using [`indels2bed.rb`](ruby_r_scripts.md#indels2bedrb), the maskIndels process scans the all-sites VCF generated by the genotypeGVCFs process for indels and generates a bed file excluding all sites a set number of bp upstream/downstream of the identified indels (`indels2bed.rb <all-sites.vcf> <indel pad in bp> > <indels.bed>`).