Mercurial > repos > stef > falco
comparison falco-filter-report.sh @ 61:77979fe362c0 draft
Uploaded
| author | stef |
|---|---|
| date | Fri, 27 Feb 2015 06:53:34 -0500 |
| parents | 73eda23fb8fd |
| children | 9f95eee38681 |
comparison
equal
deleted
inserted
replaced
| 60:2820aab8b9c8 | 61:77979fe362c0 |
|---|---|
| 18 #fi | 18 #fi |
| 19 | 19 |
| 20 ## ---------- | 20 ## ---------- |
| 21 ## set params | 21 ## set params |
| 22 ## ---------- | 22 ## ---------- |
| 23 if [[ $filter_file != 'None' && $filter_file != '' ]] # Galaxy default is "None" for some reason | 23 # if [[ $filter_file != 'None' && $filter_file != '' ]] # Galaxy default is "None" for some reason |
| 24 then | 24 # then |
| 25 FILTER_PARAM=" --filter "$filter_file | 25 # FILTER_PARAM=" --filter "$filter_file |
| 26 else | 26 # else |
| 27 FILTER_PARAM="" | 27 # FILTER_PARAM="" |
| 28 fi | 28 # fi |
| 29 | 29 |
| 30 if [[ $manifest_file != 'None' && $manifest_file != 'None' ]] # Galaxy default is "None" for some reason | 30 # if [[ $manifest_file != 'None' && $manifest_file != 'None' ]] # Galaxy default is "None" for some reason |
| 31 then | 31 # then |
| 32 MANIFEST_PARAM=" --manifest "$manifest_file | 32 # MANIFEST_PARAM=" --manifest "$manifest_file |
| 33 else | 33 # else |
| 34 MANIFEST_PARAM="" | 34 # MANIFEST_PARAM="" |
| 35 fi | 35 # fi |
| 36 | 36 |
| 37 ## name of file in galaxy not always set so will use a user-set job_name instead | 37 ## name of file in galaxy not always set so will use a user-set job_name instead |
| 38 #bam_base=`echo $bam_name | sed 's#.bam$##' - ` | 38 #bam_base=`echo $bam_name | sed 's#.bam$##' - ` |
| 39 vcf_base=$job_name | 39 vcf_base=$job_name |
| 40 | 40 |
| 41 ## ---------- | 41 ## ---------- |
| 42 ## Status / debug | 42 ## Status / debug |
| 43 ## ---------- | 43 ## ---------- |
| 44 DEBUG=1 | 44 DEBUG=1 |
| 45 if [ $DEBUG ] | 45 # if [ $DEBUG ] |
| 46 then | 46 # then |
| 47 DBS="[INFO] " | 47 # DBS="[INFO] " |
| 48 echo $DBS"FILTER: "$filter_file | 48 # echo $DBS"FILTER: "$filter_file |
| 49 echo $DBS"MANIFEST: "$manifest_file | 49 # echo $DBS"MANIFEST: "$manifest_file |
| 50 echo $DBS"REF FILE: "$REF_FILE | 50 # echo $DBS"REF FILE: "$REF_FILE |
| 51 echo $DBS"DB KEY: "$DB_KEY | 51 # echo $DBS"DB KEY: "$DB_KEY |
| 52 echo $DBS"REF SRC: "$REF_SOURCE | 52 # echo $DBS"REF SRC: "$REF_SOURCE |
| 53 echo $DBS"BAM FILE: "$bam_file | 53 # echo $DBS"BAM FILE: "$bam_file |
| 54 echo $DBS"BAM NAME: "$bam_name | 54 # echo $DBS"BAM NAME: "$bam_name |
| 55 echo $DBS"BAM BASE: "$bam_base | 55 # echo $DBS"BAM BASE: "$bam_base |
| 56 echo $DBS"OUT PATH: "$out_path | 56 # echo $DBS"OUT PATH: "$out_path |
| 57 fi | 57 # fi |
| 58 | 58 |
| 59 ## ---------- | 59 ## ---------- |
| 60 ## create output files dir | 60 ## create output files dir |
| 61 ## ---------- | 61 ## ---------- |
| 62 mkdir $out_path | 62 mkdir $out_path |