Commit 5d2e6547 authored by Karl Kornel's avatar Karl Kornel
Browse files

nextseq: Only copy sample sheet if one doesn't exist already 

If there is already a SampleSheet.csv, then don't copy over it.  Otherwise,
pick from gdrive.
parent 1bb5c1e0

bbox-workflow-nextseq

+48 −49
Original line number Diff line number Diff line
@@ -440,12 +440,18 @@ EOF 


	# Find our samplesheet

	dolog("Drive running complete!  Checking for samplesheet.\n");



    # If we have a SampleSheet.csv already, then we're fine

    if (-r "$RUNFOLDER/SampleSheet.csv") {

        dolog("A SampleSheet.csv already exists.  Not copying from gdrive\n");

    } else {

        # Build the list of candidate SampleSheet files.

    	my $samplesheet_search_path = "$DRIVEPATH/$LIBRARYID SampleSheet*.csv";

    	$samplesheet_search_path =~ s{[ ]}{\\\ }g;

    	my @samplesheets = glob $samplesheet_search_path;

    	dolog('Found ' . scalar(@samplesheets) . " candidate(s).\n");



	# Pick exactly which samplesheet to use

        # Pick exactly which samplesheet to use (if any were found).

    	my $samplesheet_path;

	    if (scalar(@samplesheets) == 0) {

		    dolog("No samplesheets found!\n");
@@ -474,14 +480,6 @@ EOF 
    	dolog("Using samplesheet at path $samplesheet_path\n");



        # Copy the SampleSheet into place

	if (-r "$RUNFOLDER/SampleSheet.csv") {

		dolog(<<"EOF");

We found an existing SampleSheet.csv.

We are renaming this to SampleSheet.csv.old.

(If that file exists, we'll add another ".old" to that one, and so on, and ....)

EOF

		directory_rename("$RUNFOLDER/SampleSheet.csv");

	}

    	File::Copy::copy($samplesheet_path, "$RUNFOLDER/SampleSheet.csv") or do {

    		dolog(<<"EOF");

We were unable to copy the SampleSheet, because of an error.
@@ -495,6 +493,7 @@ EOF 
                          $LOGPATH, \$LOG, $RealBin, $RealScript);

    	};

    	dolog("Samplesheet copied\n");

    }



	# Check to see if we have any Project directories

	my $basecalls_path = "$RUNFOLDER/Data/Intensities/BaseCalls";