From 8ed40793558e9a72a140239a78c14b8f131ea548 Mon Sep 17 00:00:00 2001
From: Lee Katz - Aspen <gzu2@cdc.gov>
Date: Wed, 10 Apr 2024 14:11:03 -0400
Subject: [PATCH] making moves for a conda package: remove Email::Stuffer and
 add in MultiQC. Remove CG-Pipeline in most places.

---
 SneakerNet.plugins/addReadMetrics.pl          |  24 ++-
 SneakerNet.plugins/assembleAll.pl             | 200 ++----------------
 SneakerNet.plugins/emailWhoever.pl            |  53 +++--
 SneakerNet.plugins/sn_crypto_assembleAll.pl   |   4 +-
 SneakerNet.plugins/sn_immediateStatus.pl      |  35 ++-
 .../sn_iontorrent_assembleAll.pl              |   6 +-
 SneakerNet.plugins/sn_report.pl               |   5 +-
 lib/perl5/SneakerNet.pm                       |  88 +++++++-
 scripts/SneakerNetPlugins.pl                  |  31 +--
 9 files changed, 182 insertions(+), 264 deletions(-)

diff --git a/SneakerNet.plugins/addReadMetrics.pl b/SneakerNet.plugins/addReadMetrics.pl
index 355966df..f583f68b 100755
--- a/SneakerNet.plugins/addReadMetrics.pl
+++ b/SneakerNet.plugins/addReadMetrics.pl
@@ -15,7 +15,7 @@
 
 use lib "$FindBin::RealBin/../lib/perl5";
 use List::MoreUtils qw/uniq/;
-use SneakerNet qw/exitOnSomeSneakernetOptions recordProperties readConfig logmsg samplesheetInfo_tsv command/;
+use SneakerNet qw/readMetrics exitOnSomeSneakernetOptions recordProperties readConfig logmsg samplesheetInfo_tsv command/;
 
 $ENV{PATH}="$ENV{PATH}:/opt/cg_pipeline/scripts";
 our $VERSION = "2.0";
@@ -30,7 +30,6 @@ sub main{
   exitOnSomeSneakernetOptions({
       _CITATION => $CITATION,
       _VERSION  => $VERSION,
-      'run_assembly_readMetrics.pl (CG-Pipeline)'   => 'echo CG-Pipeline version unknown',
     }, $settings,
   );
 
@@ -150,21 +149,24 @@ sub addReadMetrics{
 
 sub readMetricsWorker{
   my($Q, $settings)=@_;
+  
+  my %metrics;
 
   my $tempdir=tempdir("worker.XXXXXX", DIR=>$$settings{tempdir}, CLEANUP=>1);
   while(defined(my $fastq=$Q->dequeue)){
     logmsg "read metrics for $fastq";
-    eval{
-      command("run_assembly_readMetrics.pl --numcpus 1 --fast $fastq >> $tempdir/readMetrics.tsv");
-      return 1;
-    };
-    if($@){
-      logmsg "There was an error running run_assembly_readMetrics.pl.  This might be because of a divide-by-zero error. This can be solved by running the metrics without subsampling the reads which is slower.\n";
-      logmsg "Rerunning without --fast.";
-      command("run_assembly_readMetrics.pl --numcpus 1 $fastq >> $tempdir/readMetrics.tsv");
-    } 
+    my $metricsHashRef = readMetrics([$fastq]);
+    %metrics = (%metrics, %$metricsHashRef);
+  }
 
+  # Write to the output file
+  open(my $fh, ">>", "$tempdir/readMetrics.tsv") or die "ERROR: could not append to $tempdir/readMetrics.tsv: $!";
+  print $fh join("\t", qw(File avgReadLength totalBases minReadLength maxReadLength avgQuality numReads coverage))."\n";
+  while(my($fastq,$m) = each(%metrics)){
+    print $fh join("\t", basename($fastq), $$m{avgReadLength}, $$m{totalBases}, $$m{minReadLength}, 
+                         $$m{maxReadLength}, $$m{avgQuality}, $$m{numReads}, $$m{coverage}) . "\n";
   }
+  close $fh;
 }
 
 
diff --git a/SneakerNet.plugins/assembleAll.pl b/SneakerNet.plugins/assembleAll.pl
index 013b6f4d..e3ea0e14 100755
--- a/SneakerNet.plugins/assembleAll.pl
+++ b/SneakerNet.plugins/assembleAll.pl
@@ -30,8 +30,6 @@ sub main{
   exitOnSomeSneakernetOptions({
       _CITATION => $CITATION,
       _VERSION  => $VERSION,
-      'run_prediction_metrics.pl (CG-Pipeline)'     => "echo CG Pipeline version unknown",
-      'run_assembly_metrics.pl (CG-Pipeline)'       => "echo CG Pipeline version unknown",
       cat                             => 'cat --version | head -n 1',
       sort                            => 'sort --version | head -n 1',
       head                            => 'head --version | head -n 1',
@@ -80,12 +78,12 @@ sub main{
  
   mkdir "$dir/SneakerNet";
   mkdir "$dir/SneakerNet/assemblies";
-  my $metricsOut=assembleAll($dir,$settings);
-  logmsg "Metrics can be found in $metricsOut";
+  assembleAll($dir,$settings);
+  #logmsg "Metrics can be found in $metricsOut";
 
-  my $rawMultiQC = makeMultiQC($dir, $settings);
+  #my $rawMultiQC = makeMultiQC($dir, $settings);
 
-  recordProperties($dir,{version=>$VERSION,table=>$metricsOut, mqc=>$rawMultiQC,
+  recordProperties($dir,{version=>$VERSION,
     "Minimum contig length for assembly metrics" => "500bp",
   });
 
@@ -136,8 +134,7 @@ sub assembleAll{
     my $outassembly="$outdir/$sample.shovill.skesa.fasta";
     my $outgfa     ="$outdir/$sample.shovill.skesa.gfa";
     my $outgbk="$outdir/$sample.shovill.skesa.gbk";
-    #my $outassembly="$outdir/$sample.megahit.fasta";
-    #my $outgbk="$outdir/$sample.megahit.gbk";
+    my $outgff="$outdir/$sample.shovill.skesa.gff";
 
     # Run the assembly
     if(!-e $outassembly){
@@ -158,141 +155,23 @@ sub assembleAll{
       cp($assembly, $outassembly) or die "ERROR copying $assembly => $outassembly\n  $!";
       cp($gfa,      $outgfa)      or die "ERROR copying $gfa => $outgfa\n  $!";
 
-      mkdir "$outdir/prodigal"; # just make this directory right away
+      #mkdir "$outdir/prodigal"; # just make this directory right away
     }
-
-    # Genome annotation
-    logmsg "PREDICT GENES FOR SAMPLE $sample";
-    if(!-e $outgbk){
-      my $gbk=annotateFasta($sample,$outassembly,$settings);
-      cp($gbk,$outgbk) or die "ERROR: could not copy $gbk to $outgbk: $!";
-    }
-
-  }
-  
-  # run assembly metrics with min contig size=0.5kb
-  my $metricsOut="$dir/SneakerNet/forEmail/assemblyMetrics.tsv";
-  logmsg "Running metrics on the genbank files at $metricsOut";
-
-  my @thr;
-  my $Q=Thread::Queue->new(glob("$dir/SneakerNet/assemblies/*/*.shovill.skesa.gbk"));
-  for(0..$$settings{numcpus}-1){
-    $thr[$_]=threads->new(\&predictionMetricsWorker,$Q,$settings);
-    $Q->enqueue(undef);
-  }
-  for(@thr){
-    $_->join;
-  }
-  
-  command("cat $$settings{tempdir}/worker.*/metrics.tsv | head -n 1 > $metricsOut"); # header
-  #command("sort -k1,1 $$settings{tempdir}/worker.*/metrics.tsv | uniq -u >> $metricsOut"); # content
-  command("tail -q -n +2 $$settings{tempdir}/worker.*/metrics.tsv | sort | grep -Ev '^File\\b' >> $metricsOut");
-  
-  return $metricsOut;
-}
-
-sub predictionMetricsWorker{
-  my($Q,$settings)=@_;
-  my $tempdir=tempdir("worker.XXXXXX", DIR=>$$settings{tempdir}, CLEANUP=>1);
-  my $metricsOut    ="$tempdir/metrics.tsv";  # Combined metrics
-
-  #command("touch $predictionOut $assemblyOut");
-
-  my $numMetrics=0;
-  while(defined(my $gbk=$Q->dequeue)){
-    my $dir = dirname($gbk);
-    my $predictionOut ="$dir/predictionMetrics.tsv";
-    my $assemblyOut   ="$dir/assemblyMetrics.tsv";
-    my $coverageOut   ="$dir/depth.tsv.gz";
-    my $effectiveCoverage = "$dir/effectiveCoverage.tsv";
-
-    # Metrics for the fasta: the fasta file has the same
-    # base name but with a fasta extension
-    my $fasta=$gbk;
-    $fasta=~s/gbk$/fasta/;
-    my $bam  =$gbk;
-    $bam  =~s/gbk$/bam/;
     
-    # Bring the shovill bam file over
-    my $srcBam = dirname($fasta)."/shovill/shovill.bam";
-    if(!-e $bam){
-      logmsg "hard linking: $srcBam => $bam";
-      link($srcBam, $bam) or logmsg "WARNING: could not hard link $srcBam => $bam: $!";
-    }
-    
-    logmsg "gbk metrics for $gbk";
-    command("run_prediction_metrics.pl $gbk > $predictionOut");
-    logmsg "asm metrics for $fasta";
-    command("run_assembly_metrics.pl --allMetrics --numcpus 1 $fasta > $assemblyOut");
-
-    if(-e $bam){
-      logmsg "Coverage for $bam";
-      command("samtools depth -aa $bam | gzip -c > $coverageOut");
-
-      logmsg "Effective coverage for $bam";
-      my $total = 0;
-      my $numSites = 0;
-      open(my $fh, "zcat $coverageOut |") or die "ERROR: could not zcat $coverageOut: $!";
-      while(my $line = <$fh>){
-        chomp($line);
-        my(undef, undef, $depth) = split(/\t/, $line);
-        $total+=$depth;
-        $numSites++;
-      }
-      close $fh;
-      open(my $outFh, ">", $effectiveCoverage) or die "ERROR: could not write to $effectiveCoverage: $!";
-      print $outFh join("\t", qw(File effectiveCoverage))."\n";
-      print $outFh join("\t", $bam, sprintf("%0.2f", $total/$numSites))."\n";
-      close $outFh;
-    } else {
-      logmsg "WARNING: cannot determine effective coverage: could not find bam at $bam";
-      # dummy data
-      open(my $outFh, ">", $effectiveCoverage) or die "ERROR: could not write to $effectiveCoverage: $!";
-      print $outFh join("\t", qw(File effectiveCoverage))."\n";
-      print $outFh join("\t", $bam, -1)."\n";
-      close $outFh;
-    }
-
-    # Combine the metrics into one file
-    # We know that each file is one header and one values line
-    my %metric;
-    for my $file ($predictionOut, $effectiveCoverage, $assemblyOut){
-      open(my $metricsFh, $file) or die "ERROR: could not read file $file: $!";
-      my $header = <$metricsFh>;
-      my $values = <$metricsFh>;
-      chomp($header, $values);
-      close $metricsFh;
-
-      # Header and value match up
-      my @header = split(/\t/, $header);
-      my @value  = split(/\t/, $values);
-      for(my $i=0;$i<@header;$i++){
-        $metric{$header[$i]} = $value[$i];
-      }
-      # Remove the directory and suffix of the filename
-      $metric{File} = basename($metric{File}, qw(.shovill.skesa.fasta .shovill.skesa.gbk .shovill.skesa.bam));
+    if(!-e "$outdir/quast/report.html"){
+      logmsg "Running quast on $outassembly > $outdir/quast";
+      command("quast $outassembly --glimmer --output-dir $outdir/quast --threads $$settings{numcpus} --rna-finding");
     }
-    # Combine the metrics
-    # Alphabetize the header but take care of Filename separately
-    my $filename = $metric{File};
-    my @header = sort keys(%metric);
-    @header = grep{!/File/} @header;
-
-    # Write combined metrics to file
-    open(my $combinedFh, ">>", $metricsOut) or die "ERROR: could not write to $metricsOut: $!";
-    print $combinedFh join("\t", "File", @header)."\n";
-    print $combinedFh $metric{File};
-    for my $h(@header){
-      print $combinedFh "\t" . $metric{$h};
+    else{
+      logmsg "Found $outdir/quast/report.html. Not rerunning";
     }
-    print $combinedFh "\n";
-    close $combinedFh;
 
-    $numMetrics++;
   }
+  
 }
 
 
+
 sub assembleSample{
   my($sample,$sampleInfo,$settings)=@_;
 
@@ -336,59 +215,6 @@ sub assembleSample{
   return $outdir
 }
 
-# I _would_ use prokka, except it depends on having an up to date tbl2asn
-# which is not really necessary for what I'm doing here.
-sub annotateFasta{
-  my($sample,$assembly,$settings)=@_;
-
-  # Ensure a clean slate
-  my $outdir="$$settings{tempdir}/$sample/prodigal";
-  system("rm -rf $outdir");
-
-  mkdir "$$settings{tempdir}/$sample";
-  mkdir $outdir;
-
-  my $outgff="$outdir/prodigal.gff";
-  my $outgbk="$outdir/prodigal.gbk";
-
-  logmsg "Predicting genes on $sample with Prodigal";
-  eval{
-    command("prodigal -q -i $assembly -o $outgff -f gff -g 11 1>&2");
-  };
-  # If there is an issue, push ahead with a zero byte file
-  if($@){
-    logmsg "There was an issue with predicting genes on sample $sample. This might be caused by a poor assembly.";
-    open(my $fh, ">", $outgff) or die "ERROR: could not write to $outgff: $!";
-    close $fh;
-  }
-
-  # Read the assembly sequence
-  my %seqObj;
-  my $seqin=Bio::SeqIO->new(-file=>$assembly);
-  while(my $seq=$seqin->next_seq){
-    $seqObj{$seq->id}=$seq;
-  }
-  $seqin->close;
-
-  # Add seq features
-  my $gffin=Bio::FeatureIO->new(-file=>$outgff);
-  while(my $feat=$gffin->next_feature){
-    # put the features onto the seqobj and write it to file
-    my $id=$feat->seq_id;
-    $seqObj{$id}->add_SeqFeature($feat);
-  }
-  $gffin->close;
-
-  # Convert to gbk
-  my $gbkObj=Bio::SeqIO->new(-file=>">$outgbk",-format=>"genbank");
-  for my $seq(values(%seqObj)){
-    $gbkObj->write_seq($seq);
-  }
-  $gbkObj->close;
-
-  return $outgbk;
-}
-
 sub usage{
   print "Assemble all genomes
   Usage: $0 MiSeq_run_dir
diff --git a/SneakerNet.plugins/emailWhoever.pl b/SneakerNet.plugins/emailWhoever.pl
index 03112644..b60fc8fa 100755
--- a/SneakerNet.plugins/emailWhoever.pl
+++ b/SneakerNet.plugins/emailWhoever.pl
@@ -12,6 +12,7 @@
 use File::Find qw/find/;
 use Cwd qw/realpath/;
 use File::Temp qw/tempdir/;
+use MIME::Base64 qw/encode_base64/;
 use POSIX qw/strftime/;
 use IO::Compress::Zip qw(zip $ZipError);
 
@@ -19,7 +20,6 @@
 
 use Config::Simple;
 use SneakerNet qw/exitOnSomeSneakernetOptions recordProperties readConfig passfail command logmsg version/;
-use Email::Stuffer;
 use List::MoreUtils qw/uniq/;
 
 our $VERSION = "3.0";
@@ -38,7 +38,8 @@ sub main{
   exitOnSomeSneakernetOptions({
       _CITATION => $CITATION,
       _VERSION  => $VERSION,
-      sendmail  => 'sendmail -d0.4 -bv root 2>&1 | grep -m 1 Version'
+      sendmail  => 'apt-cache show sendmail 2>/dev/null | grep Version || rpm -qi sendmail 2>/dev/null | grep Version',
+      uuencode  => 'uuencode --version | grep uuencode',
     }, $settings,
   );
 
@@ -178,31 +179,27 @@ sub emailWhoever{
     $body.=$failureMessage;
   }
 
-  my $email=Email::Stuffer->from($from)
-                          ->subject($subject)
-                          ->to($to);
+  my $emailFile = "$$settings{tempdir}/email.txt";
+  open(my $fh, ">", $emailFile) or die "ERROR: could not write to $emailFile: $!";
+  print $fh "To: $to\n";
+  print $fh "From: $from\n";
+  print $fh "Subject: $subject\n";
+  print $fh "\n";
+  print $fh "$body\n";
 
-  #for my $file(glob("$dir/SneakerNet/forEmail/*")){
-  #  next if(!-f $file);
-  #  $email->attach_file($file);
-  #}
-  # Attach log files
+  # Append attachments to the email text file
   for my $file(glob("$dir/*.log")){
     next if(!-f $file);
-    $email->attach_file($file);
+    append_attachment($fh, $file);
   }
+  # Make the zip file
   my $zip = "$$settings{tempdir}/$runName.zip";
   zip_directory("$dir/SneakerNet/forEmail", $zip);
-  $email->attach_file($zip);
-  $email->attach_file("$dir/SneakerNet/forEmail/report.html");
-  $email->attach_file("$dir/SneakerNet/forEmail/multiqc_report.html");
-  $email->text_body($body);
+  append_attachment($fh, $zip);
+  append_attachment($fh, "$dir/SneakerNet/forEmail/report.html");
+  append_attachment($fh, "$dir/SneakerNet/forEmail/multiqc_report.html");
 
-  my $was_sent=$email->send;
-
-  if(!$was_sent){
-    logmsg "Warning: Email was not sent to $to!";
-  }
+  command("sendmail -t < $emailFile");
 
   return \@to;
 }
@@ -229,6 +226,22 @@ sub zip_directory {
     die "Zip failed" if $?;
 }
 
+# Add an attachment to an email file handle
+sub append_attachment {
+    my ($fh, $file_path) = @_;
+
+    # Encode the attachment content using base64 encoding
+    my $attachment_name = basename($file_path);
+    my $encoded_content = `uuencode $file_path $attachment_name`;
+    die "Failed to encode attachment content from $file_path: $!" if $?;
+    
+    print $fh $encoded_content . "\n";
+
+    # Print a newline to separate MIME parts
+    print $fh "\n";
+}
+
+
 sub usage{
   print "Email a SneakerNet run's results
   Usage: $0 run-dir
diff --git a/SneakerNet.plugins/sn_crypto_assembleAll.pl b/SneakerNet.plugins/sn_crypto_assembleAll.pl
index ec1a3fdc..088af0d9 100755
--- a/SneakerNet.plugins/sn_crypto_assembleAll.pl
+++ b/SneakerNet.plugins/sn_crypto_assembleAll.pl
@@ -30,7 +30,7 @@ sub main{
   exitOnSomeSneakernetOptions({
       _CITATION => $CITATION,
       _VERSION  => $VERSION,
-      'run_assembly_filterContigs.pl (CG-Pipeline)' => "echo CG Pipeline version unknown",
+      'seqtk'   => 'seqtk 2>&1 | grep Version',
       'run_prediction_metrics.pl (CG-Pipeline)'     => "echo CG Pipeline version unknown",
       'run_assembly_metrics.pl (CG-Pipeline)'       => "echo CG Pipeline version unknown",
       cat                             => 'cat --version | head -n 1',
@@ -111,7 +111,7 @@ sub assembleAll{
       # Save the assembly
       mkdir $outdir;
       mkdir "$outdir/prodigal"; # just make this directory right away
-      command("run_assembly_filterContigs.pl -l 500 $assembly > $outassembly");
+      command("seqtk seq -L 500 $assembly > $outassembly");
     }
 
     # Genome annotation
diff --git a/SneakerNet.plugins/sn_immediateStatus.pl b/SneakerNet.plugins/sn_immediateStatus.pl
index 2108a6e5..f491deaf 100755
--- a/SneakerNet.plugins/sn_immediateStatus.pl
+++ b/SneakerNet.plugins/sn_immediateStatus.pl
@@ -14,7 +14,6 @@
 use SneakerNet qw/exitOnSomeSneakernetOptions recordProperties readConfig samplesheetInfo_tsv command logmsg fullPathToExec/;
 
 use Text::Fuzzy;
-use Email::Stuffer;
 
 our $VERSION = "1.7";
 our $CITATION= "Immediate status report by Lee Katz";
@@ -28,7 +27,8 @@ sub main{
   exitOnSomeSneakernetOptions({
       _CITATION => $CITATION,
       _VERSION  => $VERSION,
-      sendmail  => 'sendmail -d0.4 -bv root 2>&1 | grep -m 1 Version',
+      sendmail  => 'apt-cache show sendmail 2>/dev/null | grep Version || rpm -qi sendmail 2>/dev/null | grep Version',
+      uuencode  => 'uuencode --version | grep uuencode',
     }, $settings,
   );
 
@@ -114,14 +114,15 @@ sub main{
   my $subject="Initial SneakerNet status for ".basename(File::Spec->rel2abs($dir));
   my $body = "If you see errors below, please contact the bioinformatics team with your run number and when you deposited the run. Include this file in your message.\nRun can be found at ".File::Spec->abs2rel($dir)."\n";
      $body.= "\nDocumentation can be found at https://github.com/lskatz/SneakerNet/blob/master/docs/plugins/sn_immediateStatus.pl.md\n";
-  my $email=Email::Stuffer->from($from)
-                          ->subject($subject)
-                          ->to($to)
-                          ->text_body($body)
-                          ->attach_file($outfile);
-  if(!$email->send){
-    die "ERROR: email was not sent to $to!";
-  }
+  
+  my $emailFile = "$$settings{tempdir}/email.txt";
+  open(my $fh, ">", $emailFile) or die "ERROR: could not write to $emailFile: $!";
+  print $fh "To: $to\n";
+  print $fh "From: $from\n";
+  print $fh "Subject: $subject\n";
+  print $fh "\n";
+  print $fh "$body\n\n";
+  append_attachment($fh, $outfile);
 
   recordProperties($dir,{
       version=>$VERSION, reportTo=>$to, 
@@ -183,6 +184,20 @@ sub doubleCheckRun{
   return \%errHash;
 }
 
+# Add an attachment to an email file handle
+sub append_attachment {
+    my ($fh, $file_path) = @_;
+
+    # Encode the attachment content using base64 encoding
+    my $attachment_name = basename($file_path);
+    my $encoded_content = `uuencode $file_path $attachment_name`;
+    die "Failed to encode attachment content from $file_path: $!" if $?;
+    
+    print $fh $encoded_content . "\n";
+
+    # Print a newline to separate MIME parts
+    print $fh "\n";
+}
 
 sub usage{
   print "Double check a run and its completeness. Email a report.
diff --git a/SneakerNet.plugins/sn_iontorrent_assembleAll.pl b/SneakerNet.plugins/sn_iontorrent_assembleAll.pl
index 8b9a98da..23601403 100755
--- a/SneakerNet.plugins/sn_iontorrent_assembleAll.pl
+++ b/SneakerNet.plugins/sn_iontorrent_assembleAll.pl
@@ -30,7 +30,7 @@ sub main{
   exitOnSomeSneakernetOptions({
       _CITATION => $CITATION,
       _VERSION  => $VERSION,
-      'run_assembly_filterContigs.pl (CG-Pipeline)' => "echo CG Pipeline version unknown",
+      'seqtk'   => 'seqtk 2>&1 | grep Version',
       'run_prediction_metrics.pl (CG-Pipeline)'     => "echo CG Pipeline version unknown",
       'spades.py (SPAdes)'                     => 'spades.py --version 2>&1',
       'prodigal'                      => "prodigal -v 2>&1 | grep -i '^Prodigal V'",
@@ -51,7 +51,7 @@ sub main{
   mkdir "$dir/SneakerNet/forEmail";
 
   # Check for required executables
-  for (qw(spades.py prodigal run_assembly_filterContigs.pl run_prediction_metrics.pl)){
+  for (qw(spades.py prodigal run_prediction_metrics.pl)){
     fullPathToExec($_);
   }
  
@@ -89,7 +89,7 @@ sub assembleAll{
       # Save the assembly
       mkdir $outdir;
       mkdir "$outdir/prodigal"; # just make this directory right away
-      command("run_assembly_filterContigs.pl -l 500 $assembly > $outassembly");
+      command("seqtk seq -L 500 $assembly > $outassembly");
     }
 
     # Genome annotation
diff --git a/SneakerNet.plugins/sn_report.pl b/SneakerNet.plugins/sn_report.pl
index 071d99ea..30be6655 100755
--- a/SneakerNet.plugins/sn_report.pl
+++ b/SneakerNet.plugins/sn_report.pl
@@ -7,6 +7,7 @@
 use Data::Dumper;
 use File::Basename qw/fileparse basename dirname/;
 use File::Temp qw/tempdir/;
+use File::Copy qw/cp/;
 use File::Spec;
 use Cwd qw/realpath/;
 use POSIX qw/strftime/;
@@ -147,8 +148,8 @@ sub main{
   logmsg "Report can be found in $outfile";
 
   command("multiqc --force $dir/SneakerNet/MultiQC-build --outdir $dir/SneakerNet/MultiQC.out");
-  link("$dir/SneakerNet/MultiQC.out/multiqc_report.html", "$dir/SneakerNet/forEmail/multiqc_report.html")
-    or die "ERROR: could not hard link multiqc_report.html to the forEmail folder: $!";
+  cp("$dir/SneakerNet/MultiQC.out/multiqc_report.html", "$dir/SneakerNet/forEmail/multiqc_report.html")
+    or die "ERROR: could not cp multiqc_report.html to the forEmail folder: $!";
 
   return 0;
 }
diff --git a/lib/perl5/SneakerNet.pm b/lib/perl5/SneakerNet.pm
index 421b5894..f20944cf 100644
--- a/lib/perl5/SneakerNet.pm
+++ b/lib/perl5/SneakerNet.pm
@@ -4,11 +4,14 @@ use warnings;
 use Exporter qw(import);
 use File::Basename qw/fileparse basename dirname/;
 use File::Copy qw/mv/;
+use File::Temp qw/tempdir/;
 #use File::Spec ();
 use Config::Simple;
 use Data::Dumper;
 use Carp qw/croak confess carp/;
 use Cwd qw/realpath/;
+use List::Util qw/sum min max/;
+use version 0.77;
 
 use FindBin qw/$Bin $Script $RealBin $RealScript/;
 
@@ -17,6 +20,7 @@ our @EXPORT_OK = qw(
   readTsv readKrakenDir
   command logmsg fullPathToExec version recordProperties readProperties
   exitOnSomeSneakernetOptions
+  readMetrics
   @rankOrder %rankOrder $VERSION
 );
 
@@ -32,7 +36,7 @@ TODO
 
 =cut
 
-our $VERSION  = '0.25.0';
+our $VERSION  = version->declare('0.25.0');
 our %rankName = (S=>'species', G=>'genus', F=>'family', O=>'order', C=>'class', P=>'phylum', K=>'kingdom', D=>'domain', U=>'unclassified');
 our @rankOrder= qw(S G F O C P K D U);
 our %rankOrder= (S=>0, G=>1, F=>2, O=>3, C=>4, P=>5, K=>6, D=>7, U=>8);
@@ -926,6 +930,88 @@ sub readProperties{
   return \%prop;
 }
 
+=head3 readMetrics(\@fastq, $expectedGenomeSize, $settings)
+
+Read metrics.
+Replacing CG-Pipeline's run_assembly_readMetrics.pl
+
+Arguments:
+
+  \@fastq              The list of fastq files
+  $expectedGenomeSize  in nucleotides
+  $settings            hash
+
+Returns
+
+  $properties:  hash ref with keys.  E.g.,
+    File
+    avgReadLength
+    totalBases
+    minReadLength
+    maxReadLength
+    avgQuality
+    numReads
+    coverage
+
+=cut
+
+sub readMetrics{
+  my($fastqs, $expectedGenomeSize, $settings) = @_;
+  my %metrics;
+
+  my @fastq = sort{$a cmp $b} @$fastqs;
+
+  my $tempdir = tempdir(basename($0).".readMetrics.XXXXXX",TMPDIR=>1,CLEANUP=>1);
+
+  for(my $i=0; $i<@fastq; $i++){
+    my $seqtkComp = "$tempdir/".basename($fastq[$i]).".seqtkcomp";
+    my $seqtkFqchk= "$tempdir/".basename($fastq[$i]).".seqtkfqchk";
+    command("seqtk comp $fastq[$i] > $seqtkComp");
+    command("seqtk fqchk $fastq[$i]> $seqtkFqchk");
+
+    my(@lengths,@A,@C,@G,@T);
+    open(my $fh, $seqtkComp) or die "ERROR: could not read seqtk comp file $seqtkComp: $!";
+    while(<$fh>){
+      # chomp; # <- not including the last field and so no need to remove last newline char
+      my($readName, $length, $A, $C, $G, $T) = split /\t/;
+      push(@lengths, $length);
+      push(@A, $A);
+      push(@C, $C);
+      push(@G, $G);
+      push(@T, $T);
+    }
+    close $fh;
+
+    # parse Fqchk to get average qual
+    my $avgQual = -1;
+    open(my $fh2, $seqtkFqchk) or die "ERROR: could not read seqtk fqchk file $seqtkFqchk: $!";
+    while(<$fh2>){
+      next if(!/^ALL/);
+      chomp;
+      my(undef, $bases, $A,$C,$G,$T,$N, $avgQ, $errQ, $low, $high) = split /\t/;
+      $avgQual = $avgQ;
+      last;
+    }
+    close $fh2;
+
+    my $totalBases = sum(@lengths);
+    my $numReads   = scalar(@lengths);
+    my $coverage   = -1;
+    if($expectedGenomeSize){
+      $coverage = $totalBases / $expectedGenomeSize;
+    }
+    $metrics{$fastq[$i]} = {
+      avgReadLength  => ($totalBases/$numReads),
+      totalBases     => $totalBases,
+      minReadLength  => min(@lengths),
+      maxReadLength  => max(@lengths),
+      avgQuality     => $avgQual,
+      numReads       => $numReads,
+      coverage       => $coverage,
+    };
+  }
+  return \%metrics;
+}
 
 1;
 
diff --git a/scripts/SneakerNetPlugins.pl b/scripts/SneakerNetPlugins.pl
index 841c9082..9959cffd 100755
--- a/scripts/SneakerNetPlugins.pl
+++ b/scripts/SneakerNetPlugins.pl
@@ -13,7 +13,6 @@
 use lib "$RealBin/../lib/perl5";
 use SneakerNet qw/readConfig command logmsg/;
 use Config::Simple;
-use Email::Stuffer;
 
 $ENV{PATH}="$ENV{PATH}:/opt/cg_pipeline/scripts";
 
@@ -89,13 +88,12 @@ sub main{
     
     # Run all plugins
     chdir($dir) or die "ERROR: could not change to directory $dir: $!";
+    logmsg "Changing directory to $dir";
     for my $e(@$exe){
 
       my $command="$RealBin/../SneakerNet.plugins/$e . --numcpus $$settings{numcpus}";
       $command.=" --force" if($$settings{force});
       $command.=" --tempdir $$settings{tempdir}" if($$settings{tempdir});
-      #print "$command\n\n"; next;
-      #command($command); next;
 
       if($$settings{'dry-run'}){
         logmsg $command;
@@ -110,33 +108,10 @@ sub main{
           logmsg "  ... however, --keep-going was specified and I will ignore that.";
           next;
         }
-
-        my $from=$$settings{from} || die "ERROR: need to set 'from' in the settings.conf file!";
-        my $subject="Run failed for ".basename(realpath($dir));
-        my @to;
-        if(ref($$settings{'default.emails'}) eq "ARRAY"){
-          push(@to, @{$$settings{'default.emails'}});
-        } else {
-          push(@to, $$settings{'default.emails'});
-        }
-        my $to = join(",",@to);
-        my $body = "Failed for ".realpath($dir)."\n\n";
-        $body .= "Plugin that failed was $e: $@";
-        my $email=Email::Stuffer->from($from)
-                                ->subject($subject)
-                                ->to($to)
-                                ->text_body($body);
-        if($email->send){
-          logmsg "Email sent to $to";
-        } else {
-          logmsg "ERROR email failed to send to $to";
-        }
-        return 1;
       }
-
-        
     }
-    chdir($cwd); # go back to original directory
+    chdir($cwd) or die "ERROR: could not change back to directory $cwd: $!"; # go back to original directory
+    logmsg "Changing directories from $dir, back to $cwd";
   }
   
   return 0;