Mercurial > repos > stef > falco
changeset 60:2820aab8b9c8 draft
Uploaded
| author | stef |
|---|---|
| date | Fri, 27 Feb 2015 06:31:30 -0500 |
| parents | 73eda23fb8fd |
| children | 77979fe362c0 |
| files | falco-call.xml falco-filter-report.xml falco/bin/falco falco/data/HCT-116/HCT116.bam falco/data/HCT-116/HCT116.bam.bai |
| diffstat | 5 files changed, 12 insertions(+), 5 deletions(-) [+] |
line wrap: on
line diff
--- a/falco-call.xml Wed Feb 25 08:50:56 2015 -0500 +++ b/falco-call.xml Fri Feb 27 06:31:30 2015 -0500 @@ -91,9 +91,9 @@ <outputs> <data format="html" name="html_output" label="FALCO-calling (${jobName})" /> <data format="vcf" name="vcf_output" label="FALCO-calling (${jobName}): VCF" /> - <data format="txt" name="qc_ann_qual_output" label="FALCO-calling (${jobName}): qc_ann_qual" /> - <data format="txt" name="qc2_ann_txt_output" label="FALCO-calling (${jobName}): qc2_ann" /> - <data format="txt" name="qc_targets_txt_output" label="FALCO-calling (${jobName}): qc_targets" /> + <data format="tsv" name="qc_ann_qual_output" label="FALCO-calling (${jobName}): qc_ann_qual" /> + <data format="tsv" name="qc2_ann_txt_output" label="FALCO-calling (${jobName}): qc2_ann" /> + <data format="tsv" name="qc_targets_txt_output" label="FALCO-calling (${jobName}): qc_targets" /> </outputs> <!-- ==================== -->
--- a/falco-filter-report.xml Wed Feb 25 08:50:56 2015 -0500 +++ b/falco-filter-report.xml Fri Feb 27 06:31:30 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="falco-call" name="falco-call" version="0.0.1"> +<tool id="falco-report" name="falco-report" version="0.0.1"> <requirements>
--- a/falco/bin/falco Wed Feb 25 08:50:56 2015 -0500 +++ b/falco/bin/falco Fri Feb 27 06:31:30 2015 -0500 @@ -22,9 +22,16 @@ "filter=s" => \$locifilt, "manifest=s" => \$manifest, "output=s" => \$base, - ) +) or die("Error in command line arguments\n"); +## sanity checks +unless ( -f $ref ){ + print STDERR "Genome Reference file not found [$ref]\n"; + exit 1; +} + + # Set paths to external script # TODO make modules