# HG changeset patch
# User stef
# Date 1438074446 14400
# Node ID 3141d9f2002527abb7f17928fe527dc481bc1b20
# Parent 07c810e4061ccbf987d81c11d5df5767fb95853d
Uploaded
diff -r 07c810e4061c -r 3141d9f20025 falco-filter-report.sh
--- a/falco-filter-report.sh Fri Jul 17 06:53:45 2015 -0400
+++ b/falco-filter-report.sh Tue Jul 28 05:07:26 2015 -0400
@@ -107,16 +107,29 @@
## creating galaxy history outputs
## ----------
#cp 'index.html' $html_out # this is the overview of samples html
-cp $sample_html_file $out_path # this is the sample html
-#cp $vcf_base'.html' $html_out # this is the sample html
+#cp $sample_html_file $out_path # this is the sample html
+cp $vcf_base'.html' $html_out # this is the sample html
## ----------
## copy files to keep to output path
## ----------
#cp -r ./$bam_base/*png $out_path/$bam_base/
cp -r ./* $out_path
+#cp -r ./$bam_base $out_path
#cp *.vcf $out_path; cp *.txt $out_path; cp *_std* $out_path
+## ------------------------
+## create final zip and quit with status 0 to tell galaxy all was fine
+## ------------------------
+
+if [[ $zip_to_history == 'true' ]]
+then
+ echo "[INFO] zipping output"
+ zip -r tmp.zip *.html *.xls *.tsv $vcf_base/*.png
+ cp tmp.zip $zip_out
+fi
+
+
## ----------
echo "END falco sh"
exit 0
diff -r 07c810e4061c -r 3141d9f20025 falco-filter-report.xml
--- a/falco-filter-report.xml Fri Jul 17 06:53:45 2015 -0400
+++ b/falco-filter-report.xml Tue Jul 28 05:07:26 2015 -0400
@@ -32,6 +32,14 @@
+
+
+
+
+
+
+
+
@@ -48,10 +56,12 @@
qc2_ann_txt_file=$qc2_ann_txt
qc_targets_txt_file=$qc_targets_txt
- vcf_name=$vcf.name
- html_out=$html_output
+ vcf_name="${vcf.name}"
+ html_out=${html_output}
out_path=${html_output.files_path}
job_name=$jobName
+ zip_out=${zip_output}
+ zip_to_history=$zip2history
@@ -61,6 +71,9 @@
+
+ (zip2history == 'true')
+