Mercurial > repos > stef > falco
changeset 61:77979fe362c0 draft
Uploaded
| author | stef |
|---|---|
| date | Fri, 27 Feb 2015 06:53:34 -0500 |
| parents | 2820aab8b9c8 |
| children | f2dc1009d668 |
| files | falco-filter-report.sh falco/bin/falco |
| diffstat | 2 files changed, 29 insertions(+), 25 deletions(-) [+] |
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--- a/falco-filter-report.sh Fri Feb 27 06:31:30 2015 -0500 +++ b/falco-filter-report.sh Fri Feb 27 06:53:34 2015 -0500 @@ -20,19 +20,19 @@ ## ---------- ## set params ## ---------- -if [[ $filter_file != 'None' && $filter_file != '' ]] # Galaxy default is "None" for some reason -then - FILTER_PARAM=" --filter "$filter_file -else - FILTER_PARAM="" -fi +# if [[ $filter_file != 'None' && $filter_file != '' ]] # Galaxy default is "None" for some reason +# then +# FILTER_PARAM=" --filter "$filter_file +# else +# FILTER_PARAM="" +# fi -if [[ $manifest_file != 'None' && $manifest_file != 'None' ]] # Galaxy default is "None" for some reason -then - MANIFEST_PARAM=" --manifest "$manifest_file -else - MANIFEST_PARAM="" -fi +# if [[ $manifest_file != 'None' && $manifest_file != 'None' ]] # Galaxy default is "None" for some reason +# then +# MANIFEST_PARAM=" --manifest "$manifest_file +# else +# MANIFEST_PARAM="" +# fi ## name of file in galaxy not always set so will use a user-set job_name instead #bam_base=`echo $bam_name | sed 's#.bam$##' - ` @@ -42,19 +42,19 @@ ## Status / debug ## ---------- DEBUG=1 -if [ $DEBUG ] -then - DBS="[INFO] " - echo $DBS"FILTER: "$filter_file - echo $DBS"MANIFEST: "$manifest_file - echo $DBS"REF FILE: "$REF_FILE - echo $DBS"DB KEY: "$DB_KEY - echo $DBS"REF SRC: "$REF_SOURCE - echo $DBS"BAM FILE: "$bam_file - echo $DBS"BAM NAME: "$bam_name - echo $DBS"BAM BASE: "$bam_base - echo $DBS"OUT PATH: "$out_path -fi +# if [ $DEBUG ] +# then +# DBS="[INFO] " +# echo $DBS"FILTER: "$filter_file +# echo $DBS"MANIFEST: "$manifest_file +# echo $DBS"REF FILE: "$REF_FILE +# echo $DBS"DB KEY: "$DB_KEY +# echo $DBS"REF SRC: "$REF_SOURCE +# echo $DBS"BAM FILE: "$bam_file +# echo $DBS"BAM NAME: "$bam_name +# echo $DBS"BAM BASE: "$bam_base +# echo $DBS"OUT PATH: "$out_path +# fi ## ---------- ## create output files dir
--- a/falco/bin/falco Fri Feb 27 06:31:30 2015 -0500 +++ b/falco/bin/falco Fri Feb 27 06:53:34 2015 -0500 @@ -30,6 +30,10 @@ print STDERR "Genome Reference file not found [$ref]\n"; exit 1; } +unless ( -f $ref.'.fai' ){ + print STDERR "Genome Reference index file not found [$ref\.fai]\n"; + exit 1; +} # Set paths to external script