fix for no_dup_removal issue

kundajelab · Aug 3, 2017 · fe55069 · fe55069
1 parent c817365
commit fe55069
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Showing 2 changed files with 36 additions and 30 deletions.
diff --git a/chipseq.bds b/chipseq.bds
@@ -450,23 +450,25 @@ void align_SE( int ctl, int rep, int nth_rep ) {
 		if ( is_final_stage_bam() ) return
 
 		if ( no_dup_removal ) {
-			( filt_bam_, flagstat_nodup_qc_, pbc_qc_ ) \
+			string tmp
+			( filt_bam_, tmp ) \
 				= dedup_bam( bam_, aln_o_dir, qc_o_dir, group, nth_rep )
+			wait
 		}
 		else {
 			( filt_bam_, dup_qc_, flagstat_nodup_qc_, pbc_qc_ ) \
 				= dedup_bam( bam_, aln_o_dir, qc_o_dir, group, nth_rep )			
 			dup_qc{group} = dup_qc_
 			add_file_to_table( dup_qc_, "QC and logs/$long/Dedup. log")
+			pbc_qc{group} = pbc_qc_
+			add_file_to_table( pbc_qc_, "QC and logs/$long/PBC log")
+			flagstat_nodup_qc{group} = flagstat_nodup_qc_
+			add_file_to_table( flagstat_nodup_qc_, "QC and logs/$long/Filtered flagstat log")
+			wait
+			// add to report
+			tmp_log := parse_flagstat( flagstat_nodup_qc_ )
+			deduped_reads = metric_prefix( parse_int( tmp_log{"total"} ) )
 		}
-		pbc_qc{group} = pbc_qc_
-		add_file_to_table( pbc_qc_, "QC and logs/$long/PBC log")
-		flagstat_nodup_qc{group} = flagstat_nodup_qc_
-		add_file_to_table( flagstat_nodup_qc_, "QC and logs/$long/Filtered flagstat log")
-		wait
-		// add to report
-		tmp_log := parse_flagstat( flagstat_nodup_qc_ )
-		deduped_reads = metric_prefix( parse_int( tmp_log{"total"} ) )
 	}
 
 	string tag_
@@ -636,23 +638,25 @@ void align_PE( int ctl, int rep, int nth_rep ) {
 		if ( is_final_stage_bam() ) return
 
 		if ( no_dup_removal ) {
-			( filt_bam_, flagstat_nodup_qc_, pbc_qc_ ) \
+			string tmp
+			( filt_bam_, tmp ) \
 				= dedup_bam_PE( bam_, aln_o_dir, qc_o_dir, group, nth_rep )
+			wait
 		}
 		else {
 			( filt_bam_, dup_qc_, flagstat_nodup_qc_, pbc_qc_ ) \
 				= dedup_bam_PE( bam_, aln_o_dir, qc_o_dir, group, nth_rep )			
 			dup_qc{group} = dup_qc_
 			add_file_to_table( dup_qc_, "QC and logs/$long/Dedup. log")
+			pbc_qc{group} = pbc_qc_
+			add_file_to_table( pbc_qc_, "QC and logs/$long/PBC log")
+			flagstat_nodup_qc{group} = flagstat_nodup_qc_
+			add_file_to_table( flagstat_nodup_qc_, "QC and logs/$long/Filtered flagstat log")
+			wait
+			// add to report
+			tmp_log := parse_flagstat( flagstat_nodup_qc_ )
+			deduped_reads = metric_prefix( parse_int( tmp_log{"total"} ) )
 		}
-		pbc_qc{group} = pbc_qc_
-		add_file_to_table( pbc_qc_, "QC and logs/$long/PBC log")
-		flagstat_nodup_qc{group} = flagstat_nodup_qc_
-		add_file_to_table( flagstat_nodup_qc_, "QC and logs/$long/Filtered flagstat log")
-		wait
-		// add to report
-		tmp_log := parse_flagstat( flagstat_nodup_qc_ )
-		deduped_reads = metric_prefix( parse_int( tmp_log{"total"} ) )
 	}
 
 	string tag_, bedpe
@@ -1643,16 +1647,18 @@ string html_chipseq_QC() {
 	html += "<div style='float:left'>"
 	html += html_table_multiple_logs( "Flagstat (raw) QC", false, "flagstat", groups, flagstat_qcs )
 	html += "</div>"
-	html += "<div style='float:left'>"
-	html += html_table_multiple_logs( "Flagstat (filtered) QC", false, "flagstat_filt", groups, flagstat_nodup_qcs )
-	html += "</div>"
-	html += "<div style='float:left'>"
-	html += html_table_multiple_logs( "Dup. QC", false, "dup", groups, dup_qcs )
-	html += "</div>"
-	html += "<div style='float:left'>"
-	html += html_table_multiple_logs( "Library Complexity QC", false, has_pe() ? "pbc_PE" : "pbc", groups, pbc_qcs )
-	if ( pbc_qcs.size()>0 ) html += html_help_pbc()
-	html += "</div>"
+	if ( !no_dup_removal ) {
+		html += "<div style='float:left'>"
+		html += html_table_multiple_logs( "Flagstat (filtered) QC", false, "flagstat_filt", groups, flagstat_nodup_qcs )
+		html += "</div>"
+		html += "<div style='float:left'>"
+		html += html_table_multiple_logs( "Dup. QC", false, "dup", groups, dup_qcs )
+		html += "</div>"
+		html += "<div style='float:left'>"
+		html += html_table_multiple_logs( "Library Complexity QC", false, has_pe() ? "pbc_PE" : "pbc", groups, pbc_qcs )
+		if ( pbc_qcs.size()>0 ) html += html_help_pbc()
+		html += "</div>"
+	}
 	html += "<div style='float:left'>"
 	html += html_table_multiple_logs( "Enrichment QC (strand cross-correlation measures)", false, "xcor", groups, xcor_qcs )
 	if ( xcor_qcs.size()>0 ) html += html_help_xcor( subsample_xcor, has_se(), has_pe() )

diff --git a/modules/postalign_bam.bds b/modules/postalign_bam.bds
@@ -118,7 +118,7 @@ string[] dedup_bam( string bam, string o_dir, string log_o_dir, string group, in
 	filt_bam 	:= "$prefix.filt.bam"
 
 	in	:= [ bam ]
-	out	:= no_dup_removal ? [filt_bam, map_qc, pbc_qc ] : [ nodup_bam, dup_qc, map_qc, pbc_qc ]
+	out	:= no_dup_removal ? [ filt_bam ] : [ nodup_bam, dup_qc, map_qc, pbc_qc ]
 
 	cpus 	:= (nth_dedup==1) ? -1 : nth_dedup; mem := get_res_mem(mem_dedup,nth_dedup);	timeout := get_res_wt(wt_dedup)
 
@@ -242,7 +242,7 @@ string[] dedup_bam_PE( string bam, string o_dir, string log_o_dir, string group,
 	filt_bam 	:= "$prefix.filt.bam"
 
 	in 	:= [ bam ]
-	out 	:= no_dup_removal ? [ filt_bam, map_qc, pbc_qc ] : [ nodup_bam, dup_qc, map_qc, pbc_qc ]
+	out 	:= no_dup_removal ? [ filt_bam ] : [ nodup_bam, dup_qc, map_qc, pbc_qc ]
 
 	cpus 	:= (nth_dedup==1) ? -1 : nth_dedup; mem := get_res_mem(mem_dedup,nth_dedup);	timeout := get_res_wt(wt_dedup)