initial commit

.gitignore

@@ -0,0 +1 @@
+.DS_store

README.md

@@ -1,2 +1,26 @@
 # CellrangerPipeline
 batch run for cellranger count 
+
+```
+perl batchCellrangerCounter.pl --help
+version 1.0, October 2018
+usage: batchCellrangerCounter.pl
+-f|--fastq
+	 path to FastQ files (required)
+-o|--output-dir
+	 path to output directory (required)
+-g|--genome
+	 path to genome index (required)
+-p|--opts
+	 additional Cellranger Count parameters
+-h|--help
+	 print help message
+-v|--version
+	 print current version
+```
+
+example:
+
+```
+perl batchCellrangerCounter.pl --fastq /path/to/fastq/ --output-dir /path/to/projec/cellranger_count_out/ --genome /path/to/genome/alien/cellranger/ --opts "--chemistry SC3Pv2 --localcores=32 --force-cells=7000"
+```

batchCellrangerCounter.pl

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+#!/usr/bin/perl
+
+use warnings;
+use strict;
+use Getopt::Long();
+
+sub usage($);
+sub version($);
+
+sub createBatchJob($);
+sub runCellranger($$$$);
+
+MAIN:
+{
+    # define inputs
+    my $version_tag = "version 1.0, October 2018";
+    my $version;
+    my $help;
+    my $path_fastq;
+    my $path_genome_index;
+    my $path_output;
+    my $opts_cellranger;
+
+    # set-up paramters
+    Getopt::Long::GetOptions(
+        "f|fastq=s" => \$path_fastq,
+        "o|output-dir=s" => \$path_output,
+        "g|genome=s" => \$path_genome_index,
+        "p|opts=s" => \$opts_cellranger,
+        "h|help" => \$help,
+        "v|version" => \$version
+    ) or usage("Error::invalid command line options");
+
+    # parse inputs
+    version($version_tag) if($version);
+    usage($version_tag) if($help);
+    usage("Error::path to FastQ files is required") unless defined($path_fastq);
+    usage("Error::path to output location is required") unless defined($path_output);
+    usage("Error::path to genome index is required") unless defined($path_genome_index);
+
+    # create batch job
+    my $batch_job = createBatchJob($path_fastq);
+
+    # run cellranger count
+    runCellranger($batch_job, $path_output, $path_genome_index, $opts_cellranger);
+
+}
+
+
+sub runCellranger($$$$)
+{
+    my $batch_job = $_[0];
+    my $path_output = $_[1];
+    my $path_genome_index = $_[2];
+    my $opts_cellranger = $_[3];
+
+    foreach my $id (sort keys %{$batch_job})
+    {
+        my $command = "cellranger count" .
+        " --id=" . $id .
+        " --fastqs=" . $batch_job->{$id} .
+        " --transcriptome=" . $path_genome_index .
+        " --sample=" . $id;
+        $command .= " " . $opts_cellranger if (defined($opts_cellranger));
+
+        print $command,"\n";
+        #system($command);
+
+        # move result to output folder
+        if (-d $id)
+        {
+            $path_output =~ s/\/$//g;
+            $command = "mv " . $id  . " " . $path_output . '/' . $id;
+            print $command,"\n";
+            #system($command);
+        }
+    }
+}
+
+sub createBatchJob($)
+{
+    my $path_fastq = $_[0];
+    my %tags = ();
+
+    $path_fastq =~ s/\/$//g;
+
+    opendir(my $dh, $path_fastq);
+    while (my $path_tag = readdir $dh)
+    {
+
+        my $path_full = $path_fastq . '/' . $path_tag;
+        next unless -d $path_full;
+        next if ($path_tag =~ m/^\./);
+        $tags{$path_tag} = $path_full;
+    }
+    closedir($dh);
+    return \%tags;
+}
+
+
+sub usage($)
+{
+    my $message = $_[0];
+    if (defined $message && length($message))
+    {
+        $message .= "\n" unless($message =~/\n$/);
+    }
+    my $command = $0;
+    $command =~ s#^.*/##;
+
+    print STDERR (
+        $message,
+        "usage: $command\n" .
+        "-f|--fastq\n" .
+        "\t path to FastQ files (required)\n" .
+        "-o|--output-dir\n" .
+        "\t path to output directory (required)\n" .
+        "-g|--genome\n" .
+        "\t path to genome index (required)\n" .
+        "-p|--opts\n" .
+        "\t additional Cellranger Count parameters\n" .
+        "-h|--help\n" .
+        "\t print help message\n" .
+        "-v|--version\n" .
+        "\t print current version\n"
+    );
+
+    die("\n");
+}
+
+sub version($)
+{
+    my $message = $_[0];
+    print STDERR (
+    $message,"\n",
+    "Scientific Computing Facility\n",
+    "Max-Planck Institute For Brain Research\n",
+    "bug reports to:\n",
+    "\tsciclist\@brain.mpg.de\n"
+    );
+    die("\n");
+}