# HG changeset patch
# User stef
# Date 1425049041 18000
# Node ID 3515b026d78bd7a6fbcab1e27998b22163e64203
# Parent  00f63511d177b47a552b00235b044926c7dd52b1
Uploaded

diff -r 00f63511d177 -r 3515b026d78b falco-filter-report.sh
--- a/falco-filter-report.sh	Fri Feb 27 09:45:42 2015 -0500
+++ b/falco-filter-report.sh	Fri Feb 27 09:57:21 2015 -0500
@@ -20,13 +20,6 @@
 ## ----------
 ## set params
 ## ----------
-if [[ $canonicals_file != 'None' && $canonicals_file != '' ]] # Galaxy default is "None" for some reason
-then 
-	CANONICALS_PARAM=" --canonicals "$canonicals_file
-else
-	CANONICALS_PARAM=""
-fi
-
 if [[ $vcf2_file != 'None' && $vcf2_file != '' ]] # Galaxy default is "None" for some reason
 then 
 	VCF2_PARAM=" --vcfOther "$vcf2_file
@@ -73,7 +66,7 @@
 ## running analysis
 ## ----------
 echo "[INFO] Starting FALCO reporting"
-CMD_STRING="$TOOLDIR/falco/bin/falco-filter-report --vcf $vcf_file --output $vcf_base --qc_ann_qual_txt $qc_ann_qual_file --qc2_ann_txt $qc2_ann_txt_file --qc_targets_txt $qc_targets_txt_file $VCF2_PARAM $CANONICALS_PARAM"
+CMD_STRING="$TOOLDIR/falco/bin/falco-filter-report --vcf $vcf_file --output $vcf_base --qc_ann_qual_txt $qc_ann_qual_file --qc2_ann_txt $qc2_ann_txt_file --qc_targets_txt $qc_targets_txt_file $VCF2_PARAM"
 echo "[INFO] "$CMD_STRING
 perl $CMD_STRING
 echo "[INFO] done with FALCO reporting"
diff -r 00f63511d177 -r 3515b026d78b falco-filter-report.xml
--- a/falco-filter-report.xml	Fri Feb 27 09:45:42 2015 -0500
+++ b/falco-filter-report.xml	Fri Feb 27 09:57:21 2015 -0500
@@ -44,13 +44,12 @@
       <validator type="empty_field" />
       <validator type="regex" message="This field may contain only non-whitespace characters">\S+</validator>
     </param>
-    <param name="vcf" type="data" multiple="false" optional="false" format="vcf" label="Input VCF" help="Select snpeff annotated VCF file" />
-    <param name="vcf2" type="data" multiple="false" optional="true" format="vcf" label="Input VCF (optional second)" help="FALCO pipeline is often run with samtools as second caller" />
+    <param name="vcf" type="data" multiple="false" optional="false" format="vcf" label="Input VCF" help="NOTE: VCF must be annotated with SNPEFF (should contain \"EFF\" FIELD)" />
+    <param name="vcf2" type="data" multiple="false" optional="true" format="vcf" label="Input VCF (optional second VCF)" help="NOTE: VCF must be annotated with SNPEFF (should contain \"EFF\" FIELD)" />
 
-    <param format="tsv" name="qc_ann_qual" optional="false" type="data" label="qc_ann_qual file" help=""/>
-    <param format="tsv" name="qc2_ann_txt" optional="false" type="data" label="qc2_ann_txt file" help=""/>
-    <param format="tsv" name="qc_targets_txt" optional="false" type="data" label="qc_targets_txt file" help=""/>
-    <param format="tsv" name="canonicals" optional="true" type="data" label="canonicals file" help=""/>
+    <param format="tsv" name="qc_ann_qual" optional="false" type="data" label="qc_ann_qual file" help="This file is output of the FALCO variant caller"/>
+    <param format="tsv" name="qc2_ann_txt" optional="false" type="data" label="qc2_ann_txt file" help="This file is output of the FALCO variant caller"/>
+    <param format="tsv" name="qc_targets_txt" optional="false" type="data" label="qc_targets_txt file" help="This file is output of the FALCO variant caller"/>
 
     <!-- ==================== -->
     <!-- Option to use your own bin annotations -->
diff -r 00f63511d177 -r 3515b026d78b falco/bin/falco-filter-report
--- a/falco/bin/falco-filter-report	Fri Feb 27 09:45:42 2015 -0500
+++ b/falco/bin/falco-filter-report	Fri Feb 27 09:57:21 2015 -0500
@@ -36,7 +36,6 @@
 	"vcf=s"        => \$vcf,
 	"vcfOther=s"   => \$vcfOther,
 	"output=s"     => \$base,
-	"canonicals=s" => \$canonicals,
 	"clinvar=s"    => \$clinvar,
 	"cosmic=s"     => \$cosmic,
 	"cosmicNC=s"   => \$cosmicNC,
diff -r 00f63511d177 -r 3515b026d78b falco/lib/perl/filter.pl
--- a/falco/lib/perl/filter.pl	Fri Feb 27 09:45:42 2015 -0500
+++ b/falco/lib/perl/filter.pl	Fri Feb 27 09:57:21 2015 -0500
@@ -81,15 +81,15 @@
 	$trans =~ s/\..*$//;
 	
 	## impossible to switch off these two transcript filters
-	## so comment these out if no other way provided
-	if (not exists($nm{$trans})) {
-		print STDERR "Unknown transcript: $row[$col{Gene_Name}] $trans\n";
-		next;
-	}
-	elsif ($nm{$trans} != 0) {
-		print STDERR "Non cannonical: $row[$col{Gene_Name}] $trans\n";
-		next;
-	}
+	## so commented out
+	# if (not exists($nm{$trans})) {
+	# 	print STDERR "Unknown transcript: $row[$col{Gene_Name}] $trans\n";
+	# 	next;
+	# }
+	# elsif ($nm{$trans} != 0) {
+	# 	print STDERR "Non cannonical: $row[$col{Gene_Name}] $trans\n";
+	# 	next;
+	# }
 
 	# Annotate clinincal variants and cosmic mutations