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1 #!/usr/bin/perl
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2 use strict;
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3 use warnings;
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4 use Getopt::Long;
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5 use File::Find;
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6 use File::Basename;
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7 use vars qw(@fastq_files);
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8
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9 my $dirname = dirname(__FILE__);
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10 my $pythonScript = "$dirname/rgFastQC.py";
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11 my $tool_dir = shift @ARGV;
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12 my $pythonJars = "$tool_dir/shared/jars/FastQC/fastqc";
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13
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14 # Site config
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15 my $num_threads = 32;
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16 my $fastq_sample_size = 400000;
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17 my $seq_host = "10.81.192.138";
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18 my $seq_username = "nextseq-user";
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19 my $seq_dir = "Desktop/Share";
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20
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21 #get localdir
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22 if(not -e "$tool_dir/transfer_convert_nextseq.loc"){
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23 system("cat $dirname/tool-data/transfer_convert_nextseq.loc > $tool_dir/transfer_convert_nextseq.loc");
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24 }
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25 open FILE, "$tool_dir/transfer_convert_nextseq.loc" or die "Could not open configuration file: $!\n";
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26 my @keys = split("=",<FILE>);
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27 (my $local_dir = $keys[$#keys]) =~s/\s+//g;
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28 close FILE;
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29
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30 # store arguments into variables
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31 my $runName;
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32 my $sampleSheet;
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33 my $user;
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34 my $accessFile;
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35 my $outDir;
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36 my $htmlFile;
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37 my $archiveFile;
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38
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39 GetOptions ("run=s" => \$runName,
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40 "samplesheet=s" => \$sampleSheet,
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41 "user=s" => \$user,
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42 "toolDir=s" => \$accessFile,
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43 "out=s" => \$outDir,
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44 "html=s" => \$htmlFile,
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45 "archive=s" => \$archiveFile);
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46
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47 if(not defined $runName or not defined $sampleSheet or not defined $user or not defined $accessFile or not defined $outDir or not defined $htmlFile){
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48 die "Usage: $0 -run <unique_suffix> -samplesheet <illumina.csv> -user <user\@domain in nextseq_access.conf> -toolDir <galaxy tool conf dir> ",
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49 "-out <output dir for FASTQC report> -html <FASTQC report file name> -archive <SAV files.zip>\n";
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50 }
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51
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52 $accessFile = "$accessFile/nextseq_access.conf";
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53
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54 # create access file if not already there
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55 my $command = `touch $accessFile`;
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56 open my $handle, '<', "$accessFile";
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57 chomp(my @allowed_users = <$handle>);
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58
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59 $runName = quotemeta($runName);
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60
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61 my ($out_file, $out_path, $out_ext ) = fileparse( $htmlFile, "\.[^.]*" );
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62
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63 # check to make sure $user is allowed to run script
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64 if (! ($user ~~ @allowed_users) ){
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65 die "Please ask the administrator to add $user to $accessFile in order to gain access to this tool\n";
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66 }
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67
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68 # First, sanity check the sample file
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69 open(CSV, $sampleSheet)
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70 or die "Cannot open $sampleSheet for reading: $!\n";
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71 undef $/; # slurp up whole file at once by undefining record separator
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72 my @CSV = split /\r?\n/, <CSV>; # allow different endings
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73 close(CSV);
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74 $/="\n"; # restore normal per-line reading
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75 my ($has_header, $has_reads, $has_data);
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76 for(@CSV){
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77 if(/^\[Header\]/){
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78 $has_header = 1;
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79 }
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80 elsif(/^\[Reads\]/){
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81 $has_reads = 1;
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82 }
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83 elsif(/^\[Data\]/){
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84 $has_data = 1;
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85 }
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86 }
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87 if(not defined $has_header){
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88 die "Header section is missing in sample sheet, please fix and resubmit this job\n";
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89 }
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90 if(not defined $has_reads){
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91 die "Reads section is missing in sample sheet, please fix and resubmit this job\n";
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92 }
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93 if(not defined $has_data){
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94 die "Data section is missing in sample sheet, please fix and resubmit this job\n";
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95 }
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96
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97 # Expand the catridge ID into the full run name on the remote host, input should look something like "H35VJBGXX"
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98 open(SSH, "ssh $seq_username\@$seq_host ls -1 $seq_dir |")
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99 or die "Could not run ssh login to $seq_host: $!\n";
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100 my @matchOptions;
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101 my @mismatchOptions;
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102 while(<SSH>){
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103 chomp;
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104 if(/$runName/o){
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105 push @matchOptions, $_;
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106 }
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107 else{
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108 push @mismatchOptions, $_;
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109 }
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110 }
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111 close(SSH);
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112 if(not @matchOptions){
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113 if(not @mismatchOptions){
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114 die "There was no data found on the rempote server at all, please ask the administrator to ",
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115 "check this tool's setup (currently checking $seq_username\@$seq_host:$seq_dir)\n";
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116 }
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117 # Keep only the ones not already uploaded as options
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118 @mismatchOptions = grep {not -e "$local_dir/$_"} @mismatchOptions;
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119 die "No run folder matching $runName was found at $seq_username\@$seq_host:$seq_dir, please try with another ",
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120 "run name. The following would work currently: ", join(", ", @mismatchOptions), "\n";
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121 }
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122 elsif(@matchOptions > 1){
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123 die "Ambiguous run name specification, please revise \"$runName\" to distinguish between existing datasets: ",
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124 join(", ", @matchOptions), "\n";
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125 }
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126 my $expandedRunName = $matchOptions[0]; # unambiguous, so proceed
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127
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128 # if sample already exits as a folder, die
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129 if(-e "$local_dir/$expandedRunName"){
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130 # die "Run $expandedRunName already exists on galaxy ($local_dir/$expandedRunName), cannot copy over\n";
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131 }
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132 # if not, copy to folder
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133 else{
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134 # system("scp -r $seq_username\@$seq_host\:$seq_dir/$expandedRunName $local_dir") >> 8 and die "Failed to copy from $seq_host to galaxy: scp exit status $?\n";
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135 }
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136
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137 # Put the sample sheet where it needs to be with the transfered data
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138 open(CSV, ">$local_dir/$expandedRunName/SampleSheet.csv")
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139 or die "Cannot open $local_dir/$expandedRunName/SampleSheet.csv for writing: $!\nThe data files have been transfered, but no BCL to FASTQ conversion has taken place.\n";
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140 print CSV join("\n", @CSV);
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141 close(CSV);
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142
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143 # convert bcl files to fastq
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144 #system("cd $local_dir/$expandedRunName; /export/common/programs/bcl2fastq/bin/bcl2fastq -r $num_threads -d $num_threads -p $num_threads -w $num_threads")>>8
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145 # and die "BCL to FASTQ conversion had non-zero exit status ($?). The BCL files were transfered, but FASTQ files were not generated.\n";
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146
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147 # Find the FASTQ files generated
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148 find(sub{push @fastq_files, $File::Find::name if /\.fastq.gz$/}, "$local_dir/$expandedRunName");
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149
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150 # Run FASTQC on sample of data from each lane/barcode
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151 # open output file and write html
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152 open(OUTFILE, ">$htmlFile")
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153 or die "Cannot open $htmlFile for writing: $!\n";
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154 print OUTFILE "<html><body><h1>Barcodes</h1>";
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155 system("mkdir -p $outDir");
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156
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157 # generate html plot using python tool
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158 $SIG{'PIPE'} = 'IGNORE';
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159 my $cwd = dirname(__FILE__);
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160 foreach my $file (@fastq_files){
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161 my ($barcode, $path, $ext ) = fileparse( $file, "\.fastq\.gz" );
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162 my $cmd = "gzip -cd $file | head -n $fastq_sample_size | python $pythonScript -i /dev/stdin "
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163 . "-d $outDir/$barcode/. "
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164 . "-o fastqc_report.html "
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165 . "-n \"FASTQC $barcode\" "
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166 . "-f \"FASTQ\" "
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167 . "-j \"$barcode$ext\" "
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168 . "-e $pythonJars";
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169 # Assumes the bash shell is being used
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170 open(CMD, "trap '' SIGPIPE; $cmd 2| grep -v \"Broken pipe\" |")
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171 or die "Cannot run FASTQC: $!\n";
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172 while(<CMD>){
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173 # Can safely ignore blank lines and SIGPIPE warnings
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174 next if /^\s*$/ or /Broken pipe/;
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175 print STDERR $_; # forward any other errors
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176 }
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177 close(CMD);
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178 system("perl -i.bak -pe \"s/>FastQC Report</>FastQC Report<div><a href='..\\/index.html'>Back to Table of Contents<\\\/a><\\\/div></;s/Images|Icons/./\" $outDir/$barcode/fastqc_report.html");
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179 system("unzip -o -d $outDir/$barcode -qq -j $outDir/$barcode/$barcode\_fastqc.zip $barcode\_fastqc/Icons/*.png");
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180 # append to html file
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181 print OUTFILE "<div><a href='$barcode/fastqc_report.html'>$barcode</a></div>";
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182 }
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183
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184
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185 print OUTFILE "</body></html>";
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186 close(OUTFILE);
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187 system("cp $htmlFile $outDir/index.html");
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188 system("cd $local_dir/$expandedRunName; rm $archiveFile; zip -r $archiveFile RunInfo.xml RunParameters.xml InterOp -q");
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