# 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') +