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25
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1 #!/bin/bash
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2 TOOLDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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3
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39
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4 echo "Started FALCO calling"
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25
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5
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6 ## ----------
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58
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7 ## Variables setup ($1 contains the bash config file path)
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25
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8 ## ----------
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9 source $1
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10
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11 ## ----------
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53
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12 ## make sure all is ok
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13 ## ----------
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14 if [ ! -f $REF_FILE".fai" ]
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15 then
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16 echo "No FAI index (fai) found for reference fasta [$REF_FILE]"
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17 exit "No FAI index (fai) found for reference fasta [$REF_FILE]"
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18 fi
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19
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20 ## ----------
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21 ## set params
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25
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22 ## ----------
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58
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23 if [[ $filter_file != 'None' && $filter_file != '' ]] # Galaxy default is "None" for some reason
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25
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24 then
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39
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25 FILTER_PARAM=" --filter "$filter_file
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25
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26 else
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39
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27 FILTER_PARAM=""
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25
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28 fi
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29
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30 if [[ $manifest_file != 'None' && $manifest_file != 'None' ]] # Galaxy default is "None" for some reason
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39
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31 then
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32 MANIFEST_PARAM=" --manifest "$manifest_file
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33 else
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34 MANIFEST_PARAM=""
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35 fi
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25
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36
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58
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37 ## name of file in galaxy not always set so will use a user-set job_name instead
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38 #bam_base=`echo $bam_name | sed 's#.bam$##' - `
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39 bam_base=$job_name
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40
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25
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41 ## ----------
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42 ## Status / debug
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43 ## ----------
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39
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44 DEBUG=1
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45 if [ $DEBUG ]
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46 then
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47 DBS="[INFO] "
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53
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48 echo $DBS"FILTER: "$filter_file
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49 echo $DBS"MANIFEST: "$manifest_file
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50 echo $DBS"REF FILE: "$REF_FILE
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51 echo $DBS"DB KEY: "$DB_KEY
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52 echo $DBS"REF SRC: "$REF_SOURCE
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53 echo $DBS"BAM FILE: "$bam_file
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54 echo $DBS"BAM NAME: "$bam_name
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55 echo $DBS"BAM BASE: "$bam_base
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56 echo $DBS"OUT PATH: "$out_path
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39
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57 fi
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25
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58
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59 ## ----------
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60 ## create output files dir
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61 ## ----------
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38
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62 mkdir $out_path
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25
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63
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64 ## ----------
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65 ## running analysis
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66 ## ----------
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67 echo "[INFO] Starting variant calling"
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59
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68 ## NOTE: if $FILTER_PARAM is set it includes the param name (--filter)
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69 ## NOTE: if $MANIFEST_PARAM is set it includes the param name (--manifest)
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39
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70 CALL_STRING="$TOOLDIR/falco/bin/falco --bam $bam_file --output $bam_base --ref $REF_FILE $FILTER_PARAM $MANIFEST_PARAM"
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71 echo "[INFO] "$CALL_STRING
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72 perl $CALL_STRING
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73 echo "[INFO] done with variant calling"
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25
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74
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75
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76 ## ----------
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77 ## create index html for main galaxy output
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78 ## ----------
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38
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79 echo "<!DOCTYPE html>" >> $html_out
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80 echo "<html>" >> $html_out
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81 echo "<head>" >> $html_out
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82 echo "<style>" >> $html_out
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83 echo " body{ padding: 0px 20px; }" >> $html_out
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84 echo " h1{ color: red; }" >> $html_out
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85 echo " table{ border: 1px solid black; padding: 5px }" >> $html_out
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86 echo "</style>" >> $html_out
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87 echo "</head>" >> $html_out
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88 echo "<body>" >> $html_out
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89 echo " <h1>FALCO</h1>" >> $html_out
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39
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90 echo " <p>This page is way to get output files that are not implemented in galaxy history, it is not intended to be a user-friendly way of displaying anything ;)</p>" >> $html_out
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91 #echo " <a href=\"index.html\">HTML</a>" >> $html_out
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38
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92 echo " <table><tbody>" >> $html_out
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39
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93 for file in *.vcf *.txt *stderr *stdout
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94 #for file in *
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38
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95 do
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96 lineCount=`wc -l $file | cut -f 1 -d " "`
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97 echo " <tr><td><a href=\"$file\">$file</a> has $lineCount lines</td></tr>" >> $html_out
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98 echo " <tr><td> --> " `head -1 $file` "</td></tr>" >> $html_out
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38
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99 done
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100 echo " </tbody></table>" >> $html_out
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101 echo "</body>" >> $html_out
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102 echo "</html>" >> $html_out
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25
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103
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104 ## ----------
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105 ## creating galaxy history outputs
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106 ## ----------
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107 #cp 'index.html' $html_out # this is the overview of samples html
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108 #cp $bam_base'.html' $out_path/'out.html' # this is the sample html
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39
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109 cp $bam_base'.falco.vcf' $vcf_out
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59
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110 cp $bam_base'.qc.ann.qual.txt' $qc_ann_qual_out
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111 cp $bam_base'.qc2.ann.txt' $qc2_ann_txt_out
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112 cp $bam_base'.qc.targets.txt' $qc_targets_txt_out
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25
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113
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114 ## ----------
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115 ## copy files to keep to output path
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116 ## ----------
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117 #cp -r ./$bam_base/*png $out_path/$bam_base/
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118 #cp -r ./* $out_path
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39
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119 cp *.vcf $out_path; cp *.txt $out_path; cp *_std* $out_path
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25
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120
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121 ## ----------
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122 echo "END falco sh"
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58
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123 exit 0
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