Merge branch 'dev' of https://github.com/NCI-RBL/iCLIP into dev

config/snakemake_config.yaml

@@ -71,6 +71,7 @@ seedPerReadNmax: 10000 #max number of seeds per read
 seedPerWindowNmax: 500 #max number of seeds per window
 sjdbScore: 2 #extra alignment score for alignmets that cross database junctions
 winAnchorMultimapNmax: 500 #max number of loci anchors are allowed to map to
+quantmod: 'TranscriptomeSAM' #additionnal alignment on transcriptome
 
 #########################################################################################
 # modules, container parameters

workflow/Snakefile

@@ -89,6 +89,7 @@ star_seed_read = config['seedPerReadNmax']
 star_seed_wind = config['seedPerWindowNmax']
 star_sj = config['sjdbScore']
 star_win_anchor = config['winAnchorMultimapNmax']
+star_quantmod = config['quantmod']
 
 # modules, container
 cont_dir = config['containerDir']
@@ -771,6 +772,7 @@ rule star:
         s_wind = star_seed_wind,
         s_sj = star_sj,
         s_anchor = star_win_anchor,
+        s_quantmod = star_quantmod,
         out_prefix = '{sp}_'
     envmodules:
         config['star'],
@@ -824,7 +826,8 @@ rule star:
         --seedPerReadNmax {params.s_read} \
         --seedPerWindowNmax {params.s_wind} \
         --sjdbScore {params.s_sj} \
-        --winAnchorMultimapNmax {params.s_anchor}
+        --winAnchorMultimapNmax {params.s_anchor} \
+        --quantMode {params.s_quantmod}
 
         # sort file
         samtools sort -m 80G -T $tmp_dir $tmp_dir/{params.out_prefix}Aligned.out.bam -o $tmp_dir/{params.out_prefix}Aligned.sortedByCoord.out.bam