SGE client JSV script to strip "-pe smp.pe 1" from cellranger SGE jobs

cellranger_sge.strip_pe.pl

#!/usr/bin/env perl
#
# Client JSV script from Mark Lundie for running cellranger
# pipeline
#
# Strips "-pe smp.pe 1" lines from job submission scripts
# (requests for >1 core will be kept unchanged)
#
# Include in qsub commands using -jsv PATH/TO/sge.strip_pe.pl

use strict;
use warnings;
no warnings qw/uninitialized/;

use Env qw(SGE_ROOT);
use lib "$SGE_ROOT/util/resources/jsv";
use JSV qw( :DEFAULT jsv_send_env jsv_log_info);

jsv_on_start(sub {
   jsv_send_env();
});

jsv_on_verify(sub {
   my %params = jsv_get_param_hash();

   if (exists $params{pe_name}) {
      my $nslots = $params{pe_min};
      if ($nslots lt 2) {
         jsv_del_param('pe_name');
         jsv_correct('Stripped PE from serial job.');
      }
   }

   jsv_accept();

});

jsv_main();
#!/usr/bin/env perl

use strict;
use warnings;
no warnings qw/uninitialized/;

use Env qw(SGE_ROOT);
use lib "$SGE_ROOT/util/resources/jsv";
use JSV qw( :DEFAULT jsv_send_env jsv_log_info);

jsv_on_start(sub {
   jsv_send_env();
});

jsv_on_verify(sub {
   my %params = jsv_get_param_hash();

   if (exists $params{pe_name}) {
      my $nslots = $params{pe_min};
      if ($nslots lt 2) {
         jsv_del_param('pe_name');
         jsv_correct('Stripped PE from serial job.');
      }
   }

   jsv_accept();

});

jsv_main();