diff --git a/runAssembly/Dockerfile b/runAssembly/Dockerfile
new file mode 100644
index 0000000..0a9832c
--- /dev/null
+++ b/runAssembly/Dockerfile
@@ -0,0 +1,54 @@
+FROM continuumio/miniconda3:23.5.2-0 AS build
+
+ENV container=docker
+
+# add conda channels
+RUN conda config --add channels conda-forge \
+    && conda config --add channels bioconda
+
+RUN conda init bash \
+    && . ~/.bashrc \
+    && conda create --name assembly \
+    && conda activate assembly 
+
+# install dependencies
+RUN conda install conda-libmamba-solver
+RUN conda config --set solver libmamba
+RUN conda install -n assembly -c conda-forge python=3.9
+RUN conda install -n assembly -c bioconda samtools=1.17
+RUN conda install -n assembly -c bioconda racon=1.5
+RUN conda install -n assembly -c bioconda seqtk=1.3
+RUN conda install -n assembly -c bioconda spades=3.15.5
+RUN conda install -n assembly -c bioconda minimap2=2.26
+RUN conda install -n assembly -c bioconda megahit=1.2.9
+RUN conda install -n assembly -c bioconda idba=1.1.3
+RUN conda install -n assembly -c bioconda unicycler=0.5.0
+RUN wget https://github.com/ruanjue/wtdbg2/releases/download/v2.5/wtdbg-2.5_x64_linux.tgz \
+    && tar -xvzf wtdbg-2.5_x64_linux.tgz \
+    && cp wtdbg-2.5_x64_linux/* /opt/conda/envs/assembly/bin
+RUN conda install -n assembly -c bioconda flye=2.9.2
+RUN conda install -n assembly git
+RUN conda install -c conda-forge conda-pack
+
+ADD bin/extractLongReads.pl /opt/conda/envs/assembly/bin
+ADD bin/getAvgLen.pl /opt/conda/envs/assembly/bin
+ADD bin/renameFilterFasta.pl /opt/conda/envs/assembly/bin
+
+RUN conda-pack -n assembly -o /tmp/env.tar && \
+    mkdir /venv && cd /venv && tar xf /tmp/env.tar && \
+    rm /tmp/env.tar
+
+RUN /venv/bin/conda-unpack
+
+FROM debian:latest AS runtime
+
+COPY --from=build /venv /venv
+ENV PERL5LIB=/venv/lib/perl5/core_perl
+
+
+ENV PATH="/venv/bin:$PATH"
+RUN git clone --depth 1 https://gitlab.com/chienchi/long_read_assembly.git
+ENV PATH="/long_read_assembly:$PATH"
+
+SHELL ["/bin/bash", "-c"]
+CMD /bin/bash
\ No newline at end of file
diff --git a/runAssembly/bin/extractLongReads.pl b/runAssembly/bin/extractLongReads.pl
new file mode 100755
index 0000000..870c346
--- /dev/null
+++ b/runAssembly/bin/extractLongReads.pl
@@ -0,0 +1,86 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::Basename;
+use Getopt::Long;
+
+my $paired_fasta='';
+my $single_fasta='';
+my $outputDir='';
+my $len_cutoff=350;
+
+GetOptions(
+    'p:s' => \$paired_fasta,
+    'u:s' => \$single_fasta,
+    'd=s' => \$outputDir,
+    'len:s' => \$len_cutoff
+);
+
+
+my $short_paired_fasta="short_paired.fa";
+my $short_single_fasta="short_single.fa";
+my $long_fasta="long.fa";
+
+open (my $o_paired, ">$short_paired_fasta") or die "Cannot write $short_paired_fasta\n";
+open (my $o_single, ">$short_single_fasta") or die "Cannot write $short_single_fasta\n";
+open (my $o_long, ">$long_fasta") or die "Cannot write $long_fasta\n";
+$/ = ">";
+if (-s $paired_fasta) {
+    open (my $fh, $paired_fasta) or die "$! $paired_fasta";
+    while (<$fh>)
+    { 
+        $_ =~ s/\>//g;
+        my ($id, @seq) = split /\n/, $_;
+        next if (!$id);
+        my ($id2, @seq2) = split /\n/, <$fh>;
+        my $seq = join "", @seq;
+        my $seq2 = join "", @seq2;
+        my $len = length($seq);
+        my $len2 = length($seq2);
+        if ($len > $len_cutoff and $len2 > $len_cutoff)
+        {
+                print $o_long ">$id\n$seq\n>$id2\n$seq2\n";
+        }
+        elsif ($len > $len_cutoff)
+        {
+                print $o_long ">$id\n$seq\n";
+                print $o_single ">$id2\n$seq2\n";
+        }
+        elsif ($len2 > $len_cutoff)
+        {
+                print $o_long ">$id2\n$seq2\n";
+                print $o_single ">$id\n$seq\n";
+        }
+        else
+        {
+                print $o_paired ">$id\n$seq\n>$id2\n$seq2\n";   
+        }
+    }
+    close $fh;
+}
+if (-s $single_fasta)
+{
+    open (my $fh, $single_fasta) or die "$! $single_fasta";
+    while (<$fh>)
+    { 
+        $_ =~ s/\>//g;
+        my ($id, @seq) = split /\n/, $_;
+        next if (!$id);
+        my $seq = join "", @seq;
+        my $len = length($seq);
+        if ($len > $len_cutoff)
+        {
+                print $o_long ">$id\n$seq\n";
+        }
+        else
+        {
+                print $o_single ">$id\n$seq\n";
+        }
+    }
+    close $fh;
+}
+$/="\n";
+close $o_paired;
+close $o_long;
+close $o_single;
\ No newline at end of file
diff --git a/runAssembly/bin/getAvgLen.pl b/runAssembly/bin/getAvgLen.pl
new file mode 100755
index 0000000..1333951
--- /dev/null
+++ b/runAssembly/bin/getAvgLen.pl
@@ -0,0 +1,198 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::Basename;
+use Getopt::Long;
+
+my $outputDir='';
+
+my @unpairedList= ();
+my @pairedList=  ();
+
+GetOptions(
+    'u:s{1,}' => \@unpairedList,
+    'p:s{1,}' => \@pairedList,
+    'd=s' => \$outputDir,
+);
+
+
+my $all_R1_fastq = "$outputDir/all.1.fastq";
+my $all_R2_fastq = "$outputDir/all.2.fastq";
+my $all_SE_fastq = "$outputDir/all.se.fastq";
+my $count_file_list= "$outputDir/fastqCount.txt";
+my $avg_read_len= 0 ;
+my $PE_count = 0 ;
+my $PE_total_len = 0;
+my $SE_count= 0 ;
+my $SE_total_len = 0 ;
+
+
+
+open (my $fh, ">$count_file_list") or die "Cannot write $count_file_list\n";
+while(my ($R1,$R2) = splice (@pairedList,0,2))
+{
+    ($PE_count, $PE_total_len) = &countPE_exe($R1,$R2,$all_R1_fastq,$all_R2_fastq,$all_SE_fastq,$fh);
+}
+foreach my $file (@unpairedList)
+{
+    ($SE_count,$SE_total_len)=&countFastq_exe($file,$all_SE_fastq);
+    printf $fh ("%s\t%d\t%d\t%.2f\n",basename($file),$SE_count,$SE_total_len,$SE_total_len/$SE_count);
+    printf ("%s\t%d\t%d\t%.2f\n",basename($file),$SE_count,$SE_total_len,$SE_total_len/$SE_count);
+}
+close $fh;
+$avg_read_len = ($PE_count + $SE_count) > 0 ? ($PE_total_len + $SE_total_len) / ($PE_count + $SE_count) : 0 ;
+
+sub countPE_exe{
+    my $r1=shift;
+    my $r2=shift;
+    my $out_r1=shift;
+    my $out_r2=shift;
+    my $out_se=shift;
+    my $count_fh=shift;
+    my %seq_hash;
+    my $pair_char;
+    my $unpaired_count=0;
+    my $read1_count=0;
+    my $read2_count=0;
+    my $se2_count=0;
+    my $se1_count=0;
+    my $paired_count=0;
+    my $read1_total_len=0;
+    my $read2_total_len=0;
+    my $existed_id1=0;
+    my $existed_id2=0;
+    my ($fh1,$pid) = open_file($r1);
+    open (my $ofh1, ">>$out_r1") or die "Cannot write $out_r1\n";
+    open (my $ofh2, ">>$out_r2") or die "Cannot write $out_r2\n";
+    open (my $ofhse, ">>$out_se") or die "Cannot write $out_se\n";
+    while(<$fh1>){
+        chomp;
+        next unless $_ =~ /\S/;
+        next if ($_ =~ /length=0/);
+        my $id_line=$_;
+        my ($id) = $id_line =~ /^\@(\S+).?\/?1?\s*/;
+        my $seq = <$fh1>;
+        chomp $seq;
+        if ($seq_hash{$id}){
+            $existed_id1++;
+        }
+        my $len = length $seq;
+        $read1_total_len += $len;
+        my $qual_id = <$fh1>;
+        my $qual = <$fh1>;
+        $seq = $seq."\n".$qual_id.$qual;
+        $seq_hash{$id}++;
+        $read1_count++;
+    }
+    close $fh1;
+    my %seq_hash2;
+    my ($fh2,$pid2) = open_file($r2);
+    while(<$fh2>){
+        chomp;
+        next unless $_ =~ /\S/;
+        next if ($_ =~ /length=0/);
+        my $id_line=$_;
+        my ($id2) = $id_line =~ /^\@(\S+)\.?\/?2?\s*/;
+        $read2_count++;
+        my $seq2 = <$fh2>;
+        chomp $seq2;
+        if ($seq_hash2{$id2}){
+            $existed_id2++;
+        }
+        my $len = length $seq2;
+        $read2_total_len += $len;
+        my $qual_id = <$fh2>;
+        my $qual = <$fh2>;
+        $seq2 = $seq2."\n".$qual_id.$qual;
+        $seq_hash2{$id2}++;
+        if ($seq_hash{$id2}){
+            $seq_hash{$id2}++;
+            $paired_count++;
+            print $ofh2 $id_line,"\n",$seq2;
+        }else{
+            print $ofhse $id_line,"\n",$seq2;
+            $se2_count++;
+        }
+    }
+    close $fh2;
+    ($fh1,$pid) = open_file($r1);
+    while(<$fh1>){
+        chomp;
+        next unless $_ =~ /\S/;
+        next if ($_ =~ /length=0/);
+        my $id_line=$_;
+        my ($id) = $id_line =~ /^\@(\S+)\.?\/?1?\s*/;
+        my $seq = <$fh1>;
+        chomp $seq;
+        my $qual_id = <$fh1>;
+        my $qual = <$fh1>;
+        $seq = $seq."\n".$qual_id.$qual;
+        if ($seq_hash{$id} == 2){
+                print $ofh1 $id_line,"\n",$seq;
+        }
+        if ($seq_hash{$id} == 1){
+                print $ofhse $id_line,"\n",$seq;
+                $se1_count++;
+        }
+    }
+    close $fh1;
+    close $ofh1;
+    close $ofh2;
+    close $ofhse;
+    printf ("%s\t%d\t%d\t%.2f\n",basename($r1),$read1_count,$read1_total_len,$read1_total_len/$read1_count);
+    printf ("%s\t%d\t%d\t%.2f\n",basename($r2),$read2_count,$read2_total_len,$read2_total_len/$read2_count);
+    printf $count_fh ("%s\t%d\t%d\t%.2f\n",basename($r1),$read1_count,$read1_total_len,$read1_total_len/$read1_count);
+    printf $count_fh ("%s\t%d\t%d\t%.2f\n",basename($r2),$read2_count,$read2_total_len,$read2_total_len/$read2_count);
+    printf ("%d duplicate id from %s\n", $existed_id1, basename($r1)) if ($existed_id1 > 0);
+    printf ("%d duplicate id from %s\n", $existed_id2, basename($r2)) if ($existed_id2 > 0);
+    printf ("There are %d reads from %s don't have corresponding paired read.\n", $se1_count, basename($r1)) if ($se1_count >0); 
+    printf ("There are %d reads from %s don't have corresponding paired read.\n", $se2_count, basename($r2)) if ($se2_count >0);
+   
+    unlink $out_se if (-z $out_se);
+    return ($read1_count + $read2_count, $read1_total_len + $read2_total_len);
+}
+
+sub countFastq_exe 
+{
+    my $file=shift;
+    my $output=shift;
+    my $seq_count=0;
+    my $total_length;
+    my ($fh,$pid)= open_file($file);
+    open (my $ofh, ">>$output") or die "Cannot write $output\n";
+    while (<$fh>)
+    { 
+        next unless $_ =~ /\S/;
+	next if ($_ =~ /length=0/);
+        my $id=$_;
+        $id = '@'."seq_$seq_count\n" if ($id =~ /No name/);
+        my $seq=<$fh>;
+        chomp $seq;
+        my $q_id=<$fh>;
+        my $q_seq=<$fh>;
+        my $len = length $seq;
+        $seq_count++;
+        $total_length +=$len;
+        print $ofh "$id$seq\n$q_id$q_seq";
+    }
+    close $fh;
+    return ($seq_count,$total_length);
+}
+
+sub touchFile{
+    my $file=shift;
+    open (my $fh,">",$file) or die "$!";
+    close $fh;
+}
+
+sub open_file
+{
+    my ($file) = @_;
+    print "$file\n"; 
+    my $fh;
+    my $pid;
+    if ( $file=~/\.gz\.?\d?$/i ) { $pid=open($fh, "gunzip -c $file |") or die ("gunzip -c $file: $!"); }
+    else { $pid=open($fh,'<',$file) or die("$file: $!"); }
+    return ($fh,$pid);
+}
\ No newline at end of file
diff --git a/runAssembly/bin/renameFilterFasta.pl b/runAssembly/bin/renameFilterFasta.pl
new file mode 100755
index 0000000..605d86a
--- /dev/null
+++ b/runAssembly/bin/renameFilterFasta.pl
@@ -0,0 +1,95 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::Basename;
+use Getopt::Long;
+
+
+my $fasta;
+my $outputDir;
+my $size_filter;
+my $max_seq_number;
+my $id_mapping;
+my $contig_size_for_annotation;
+my $project_name;
+my $do_annotation;
+
+GetOptions(
+    'u=s{1,}' => \$fasta,
+    'd=s' => \$outputDir,
+    'filt=i' => \$size_filter,
+    'maxseq=i' => \$max_seq_number,
+    'id:s' => \$id_mapping,
+    'ann_size=i' => \$contig_size_for_annotation,
+    'n=s' => \$project_name,
+    'ann:i' => \$do_annotation #default to false (0)
+);
+
+my $output= "$outputDir/${project_name}_contigs.fa";
+my $id_map= "$outputDir/id_map.txt";
+my $contig_for_annotation = "$outputDir/${project_name}_contigs_${contig_size_for_annotation}up.fa";
+$max_seq_number ||= 100000;
+my $serial_id= "0" x length($max_seq_number);
+my $id_info;
+my ($fh,$pid)=open_file($fasta);
+open (my $ofh, "> $output") or die "Cannot write $output\n";
+open (my $ofh2, "> $contig_for_annotation" ) or die "Cannot write $contig_for_annotation\n";
+open (my $idmap_ofh, "> $id_map") or die "Cannot write $id_map\n";
+$/ = ">";
+while (my $line=<$fh>)
+{
+        $line =~ s/\>//g;
+        my ($id, @seq) = split /\n/, $line;
+        next if (!$id);
+        ($id_info) = $id =~ /(length_\d+ read_count_\d+)/;
+        my $seq = join "", @seq;
+        $seq =~ s/-//g;
+        $seq =~ s/ //g;
+        $seq =~ s/\n//g;
+        $seq =~ s/\r//g;
+        $seq = uc($seq);
+        my $len = length($seq);
+        my $GC_num = $seq=~ tr/GCgc/GCgc/; 
+        my $GC_content = sprintf("%.2f",$GC_num/$len);
+        $id_info = "length_$len "if (!$id_info);
+        next if ($len < $size_filter);
+        $seq =~ s/(.{70})/$1\n/g; 
+        chomp $seq;
+        my $fasta_header;
+    $id =~ s/\W/_/g;
+        if($do_annotation){
+            # genbank format limit the LOCUS name length
+            if ($id_mapping){
+                $fasta_header = ( length($id) > 20 ) ? "contig_$serial_id $id" : "$id contig_$serial_id";
+                print $idmap_ofh "contig_$serial_id\t$id\n";
+            }else{
+                $fasta_header = ( length($project_name) > 20 || $project_name =~/^Assembly/i ) ? "contig_$serial_id $id_info GC_content_$GC_content": "${project_name}_$serial_id $id_info GC_content_$GC_content";
+            }
+        }else{
+        $fasta_header = ($id_mapping)? "$id" : "${project_name}_$serial_id $id_info GC_content_$GC_content";
+        }
+        if ($len >= $contig_size_for_annotation)
+        {
+        print $ofh2 ">$fasta_header\n" . $seq."\n";
+        }
+        print $ofh ">$fasta_header\n" . $seq."\n";
+        $serial_id++; 
+}    
+$/="\n";
+close $fh;
+close $ofh;
+close $ofh2;
+#close $idmap_ofh if ($id_mapping && $configuration->{DoAnnotation});
+if ( -z $id_map) { unlink $id_map ; }
+
+sub open_file
+{
+    my ($file) = @_;
+    print "$file\n"; 
+    my $fh;
+    my $pid;
+    if ( $file=~/\.gz\.?\d?$/i ) { $pid=open($fh, "gunzip -c $file |") or die ("gunzip -c $file: $!"); }
+    else { $pid=open($fh,'<',$file) or die("$file: $!"); }
+    return ($fh,$pid);
+}
\ No newline at end of file
diff --git a/runAssembly/nextflow.config b/runAssembly/nextflow.config
new file mode 100644
index 0000000..04c17d9
--- /dev/null
+++ b/runAssembly/nextflow.config
@@ -0,0 +1,48 @@
+process.container = 'apwat/run_assembly:1.4.5'
+singularity  {
+    enabled = true
+    runOptions = "--compat"
+}
+params {
+    assembler = "IDBA_UD"
+    outDir = '.'
+    threads = 8 
+    projName = "project"
+    annotation = false
+    contigSizeForAnnotation = 700
+    pairedFiles = "nf_assets/NO_FILE"
+    unpairedFile = "nf_assets/NO_FILE2"
+    minContigSize = 200
+    memLimit = null
+    idba{
+        maxK = null
+        minK = 31
+        step = 20
+    }
+    spades {
+        pacbio = "nf_assets/NO_FILE3"
+        nanopore = "nf_assets/NO_FILE4"
+        algorithm = null
+    }
+    megahit {
+        preset = null
+    }
+    unicycler {
+        longreads = "nf_assets/NO_FILE3"
+        minLongReads = 2000
+        bridgingMode = "normal"
+    }
+    lrasm {
+        minLength = 400
+        preset = null
+        algorithm = null
+        ec = null
+        numConsensus = null
+    }
+}
+workflow.onComplete = {
+    "rm -rf nf_assets".execute().text
+}
+workflow.onError = {
+    "rm -rf nf_assets".execute().text
+}
\ No newline at end of file
diff --git a/runAssembly/runAssembly.nf b/runAssembly/runAssembly.nf
new file mode 100644
index 0000000..e9e005d
--- /dev/null
+++ b/runAssembly/runAssembly.nf
@@ -0,0 +1,576 @@
+#!/usr/bin/env nextflow
+//to run: nextflow run runAssembly.nf -params-file [JSON parameter file]
+
+//this workflow is unable to set memory limits (used in idba and spades assemblies) by itself, 
+//but a limit (in KB) can be provided as a parameter.
+
+//main process for assembly with IDBA
+process idbaUD {
+    publishDir (
+    path:"$params.outDir/AssemblyBasedAnalysis",
+    mode: 'copy',
+    saveAs: {
+        filename ->
+        if(filename ==~ /log/) {
+            "assembly.log"
+        }
+        else if(filename ==~ /scaffold(s|-level-2|)\.fa(sta)?/) {
+            "scaffold.fa"
+        }
+        else{
+            null //do not publish contig-max.fa or intermediate contigs yet, but use them for downstream processes
+        }
+    }
+    )
+
+    input:
+    path short_paired
+    path short_single
+    path long_reads
+    val avg_len
+
+    output:
+    path "log"
+    path "scaffold*.{fa,fasta}", optional:true 
+    path "contig-max.fa", emit: contigs, optional:true
+    path "{contig-*,*contigs.fa,K*/final_contigs.fasta}", emit: intContigs
+
+    script:
+    def avg_len = avg_len as Integer
+    def runFlag = ""
+    if(short_paired.name != "NO_FILE" && short_single.name != "NO_FILE2") {
+        runFlag = "-r $short_single --read_level_2 $short_paired "
+    }
+    else if(short_paired.name != "NO_FILE") {
+        runFlag = "-r $short_paired "
+    }
+    else if(short_single.name != "NO_FILE2") {
+        runFlag = "-r $short_single "
+    }
+    def longReadsFile = long_reads.name != "NO_FILE3" ? "-l $long_reads" : ""
+    def maxK = 121
+    def maxK_option = "--maxk $maxK "
+    if (params.idba.maxK == null || params.idba.maxK > avg_len) {
+        if(avg_len > 0 && avg_len <= 151) {
+            maxK = avg_len - 1
+            maxK_option = "--maxk ${avg_len - 1}"
+        }
+    }
+    def minK = params.idba.minK != null ? "--mink $params.idba.minK " : ""
+    def step = params.idba.step != null ? "--step $params.idba.step " : ""
+    def minLen = params.minContigSize != null ? "--min_contig $params.minContigSize " : ""
+
+    def memLimit = params.memLimit != null ? "ulimit -v $params.memLimit 2>/dev/null;" : ""
+    """
+    ${memLimit}idba_ud --pre_correction -o . --num_threads $params.threads\
+    $runFlag\
+    $longReadsFile\
+    $maxK_option\
+    $minK\
+    $step\
+    $minLen
+
+    mv contig-${maxK}.fa contig-max.fa
+    """
+
+}
+
+//prep for idba
+process idbaExtractLong {
+    input:
+    path paired
+    path unpaired
+
+    output:
+    path "short_paired.fa"
+    path "short_single.fa"
+    path "long.fa"
+
+    script:
+    def pair_file = paired.name != "NO_FILE" ? "-p $paired " : ""
+    def unpaired_file = unpaired.name != "NO_FILE2" ? "-u $unpaired " : ""
+    """
+    extractLongReads.pl\
+    $pair_file\
+    $unpaired_file\
+    -d .
+    """
+}
+
+//prep for idba
+process idbaPrepReads {
+    input:
+    path paired
+    path unpaired
+
+    output:
+    path "pairedForAssembly.fasta", emit:idba_prep_paired
+    path "unpairedForAssembly.fasta", optional:true
+
+    script:
+    def pair_process = paired.name != "NO_FILE" ? "fq2fa --filter --merge ${paired[0]} ${paired[1]} pairedForAssembly.fasta;" : "" 
+    def unpair_process = unpaired.name != "NO_FILE2" ? "fq2fa --filter $unpaired unpairedForAssembly.fasta;" : "" 
+    
+    """
+    $pair_process
+    $unpair_process
+    """
+
+}
+
+//prep for idba
+process idbaReadFastq {
+    input:
+    path paired
+    path unpaired
+
+    output:
+    path "fastqCount.txt"
+
+    script:
+    def paired_list = paired.name != "NO_FILE" ? "-p ${paired}" : ""
+    def unpaired_list = unpaired.name != "NO_FILE2" ? "-u ${unpaired}" : ""
+
+    """
+    getAvgLen.pl\
+    $paired_list\
+    $unpaired_list\
+    -d .
+    """
+}
+
+//prep for idba
+process idbaAvgLen {
+    input:
+
+    path countFastq
+
+    output:
+    stdout
+
+    shell:
+    '''
+    #!/usr/bin/env perl
+    my $fastq_count_file = "./!{countFastq}";
+    my $total_count = 0;
+    my $total_len = 0;
+    open (my $fh, "<", $fastq_count_file) or die "Cannot open $fastq_count_file\n";
+    while(<$fh>){
+        chomp;
+        my ($name,$count,$len,$avg) = split /\t/,$_;
+        $total_count += $count;
+        $total_len += $len;
+    }
+    close $fh;
+    my $avg_len = ($total_count > 0)? $total_len/$total_count : 0;
+    print "$avg_len";
+    '''
+}
+
+//assemble using spades
+process spades {
+
+    publishDir (
+    path: "$params.outDir/AssemblyBasedAnalysis", 
+    mode: 'copy',
+    saveAs: {
+        filename ->
+        if(filename ==~ /spades\.log/) {
+            "assembly.log"
+        }
+        else if(filename ==~ /scaffold(s|-level-2|)\.fa(sta)?/) {
+            "scaffold.fa"
+        }
+        else if(filename ==~ /assembly_graph\.fastg/) {
+            "${params.projName}_contigs.fastg"
+        }
+        else if(filename ==~ /assembly_graph_with_scaffolds\.gfa/) {
+            "assembly_graph_with_scaffolds.gfa"
+        }
+        else if(filename ==~ /(contigs|transcripts)\.fasta/) {
+            null //do not publish contigs, but use downstream
+        }
+        else if(filename ==~ /((contig-.*)|(.*contigs\.fa)|(K.*\/final_contigs\.fasta))/) {
+            null //do not publish intermediate contigs, but use downstream
+        }
+        else{
+            filename
+        }
+    }
+    )
+
+    input:
+    path paired
+    path unpaired
+    path pacbio
+    path nanopore
+
+    output:
+    path "scaffold*.{fa,fasta}", optional:true 
+    path "spades.log" 
+    path "contigs.paths"
+    path "{contigs,transcripts}.fasta", emit:contigs, optional:true
+    path "assembly_graph.fastg", optional:true
+    path "assembly_graph_with_scaffolds.gfa", optional:true
+    path "{contig-*,*contigs.fa,K*/final_contigs.fasta}", emit: intContigs
+
+
+    script:
+    def paired = paired.name != "NO_FILE" ? "--pe1-1 ${paired[0]} --pe1-2 ${paired[1]} " : ""
+    def unpaired = unpaired.name != "NO_FILE2" ? "--s1 $unpaired " : ""
+    def pacbio_file = pacbio.name != "NO_FILE3" ? "--pacbio $pacbio " : ""
+    def nanopore_file = nanopore.name != "NO_FILE4" ? "--nanopore $nanopore " : ""
+    def meta_flag = (paired != "" && params.spades.algorithm == "metagenome") ? "--meta " : ""
+    def sc_flag = params.spades.algorithm == "singlecell" ? "--sc " : ""
+    def rna_flag = params.spades.algorithm == "rna" ? "--rna " : ""
+    def plasmid_flag = params.spades.algorithm == "plasmid" ? "--plasmid " : ""
+    def bio_flag = params.spades.algorithm == "bio" ? "--bio " : ""
+    def corona_flag = params.spades.algorithm == "corona" ? "--corona " : ""
+    def metaviral_flag = params.spades.algorithm == "metaviral" ? "--metaviral " : ""
+    def metaplasmid_flag = params.spades.algorithm == "metaplasmid" ? "--metaplasmid " : ""
+    def rnaviral_flag = params.spades.algorithm == "rnaviral" ? "--rnaviral " : ""
+    def memLimit = params.memLimit != null ? "-m ${params.memLimit/1024*1024}" : ""
+
+    """
+    spades.py -o . -t $params.threads\
+    $paired\
+    $meta_flag\
+    $sc_flag\
+    $rna_flag\
+    $plasmid_flag\
+    $bio_flag\
+    $corona_flag\
+    $metaviral_flag\
+    $metaplasmid_flag\
+    $rnaviral_flag\
+    $unpaired\
+    $pacbio_file\
+    $nanopore_file\
+    $memLimit
+    """
+}
+
+//assemble using megahit
+process megahit {
+
+    publishDir(
+    path: "$params.outDir/AssemblyBasedAnalysis", 
+    mode: 'copy',
+    saveAs: {
+        filename ->
+        if(filename.equals("megahit/log")) {
+            "assembly.log"
+        }
+        else if(filename ==~ /megahit\/scaffold(.*)\.fa(sta)?/) {
+            "scaffold.fa"
+        }
+        else if(filename ==~ /megahit\/final\.contigs\.fa/) {
+            null //don't publish, but pass to downstream "renameFilterFasta" process
+        }
+        else if(filename ==~ /megahit\/((contig-.*)|(.*contigs\.fa)|(K.*\/final_contigs\.fasta))/) {
+            null //do not publish intermediate contigs, but use downstream
+        }
+        else{
+            filename
+        }
+    }
+    )
+
+    input:
+    path paired
+    path unpaired
+
+    output:
+    path "megahit/log"
+    path "megahit/scaffold*.{fa,fasta}", optional:true //I don't believe this is a normal output of megahit, but just in case
+    path "megahit/final.contigs.fa", emit: contigs, optional:true
+    path "${params.projName}_contigs.fastg"
+    path "megahit/{contig-*,*contigs.fa,K*/final_contigs.fasta}", emit: intContigs
+
+    script:
+    def paired = paired.name != "NO_FILE" ? "-1 ${paired[0]} -2 ${paired[1]} " : ""
+    def unpaired = unpaired.name != "NO_FILE2" ? "-r $unpaired " : ""
+    def megahit_preset = params.megahit.preset != null ? "--presets $params.megahit.preset " : ""
+
+    """
+    megahit -o ./megahit -t $params.threads\
+    $megahit_preset\
+    $paired\
+    $unpaired\
+    2>&1
+
+    LARGESTKMER=\$(head -n 1 megahit/final.contigs.fa | perl -ne '/^>k(\\d+)\\_/; print \$1;')
+
+    megahit_toolkit contig2fastg \$LARGESTKMER megahit/intermediate_contigs/k\${LARGESTKMER}.contigs.fa  > ${params.projName}_contigs.fastg
+    """
+
+}
+
+
+//assembly using unicycler
+process unicycler {
+    publishDir (
+        path: "$params.outDir/AssemblyBasedAnalysis", 
+        mode: 'copy',
+        saveAs: {
+        filename ->
+        if(filename ==~ /unicycler\.log/) {
+            "assembly.log"
+        }
+        else if(filename ==~ /scaffold(s|-level-2|)\.fa(sta)?/) {
+            "scaffold.fa"
+        }
+        else if(filename.equals("assembly.gfa")) {
+            "${params.projName}_contigs.fastg"
+        }
+        else if(filename ==~ /assembly\.fasta/) {
+            null //don't publish, but emit for use in downstream process "renameFilterFasta"
+        }
+        else{
+            filename
+        }
+    }
+    )
+
+    input:
+    path paired
+    path unpaired
+    path longreads //If present, expects filtered long reads.
+
+    output:
+    path "unicycler.log"
+    path "scaffold*.{fa,fasta}", optional:true //I don't believe this is a normal output of unicycler, but just in case
+    path "assembly.fasta", emit: contigs
+    path "assembly.gfa", optional:true
+    //path "{contig-*,*contigs.fa,K*/final_contigs.fasta}", emit: intContigs | not produced by unicycler
+
+    script:
+    def paired = paired.name != "NO_FILE" ? "-1 ${paired[0]} -2 ${paired[1]} " : ""
+    def unpaired = unpaired.name != "NO_FILE2" ? "-r $unpaired " : ""
+    def filt_lr = longreads.name != "NO_FILE3" ? "-l $longreads " : ""
+    def bridge = params.unicycler.bridgingMode != "normal" ? "--mode $params.unicycler.bridgingMode" : "--mode normal"
+
+    """
+    export _JAVA_OPTIONS='-Xmx20G'; export TERM='xterm';
+
+    unicycler -t $params.threads -o .\
+    $paired\
+    $filt_lr\
+    $bridge 2>&1 1>/dev/null
+    """
+
+}
+
+//filter long reads for unicycler
+process unicyclerPrep {
+    input:
+    path longreads
+
+
+    output:
+    path "long_reads.fasta"
+
+    script:
+
+    """
+    seqtk seq -A -L\
+    $params.unicycler.minLongReads\
+    $longreads > long_reads.fasta
+    """
+}
+
+
+//assembly using lrasm
+process lrasm {
+
+    publishDir (
+        path: "$params.outDir/AssemblyBasedAnalysis", 
+        mode: 'copy',
+        saveAs: {
+        filename ->
+        if(filename ==~ /contigs\.log/) {
+            "assembly.log"
+        }
+        else if(filename ==~ /scaffold(s|-level-2|)\.fa(sta)?/) {
+            "scaffold.fa"
+        }
+        else if(filename.equals("Assembly/unitig.gfa")) {
+            "${params.projName}_contigs.fastg"
+        }
+        else if(filename.equals("Assembly/assembly_graph.gfa")) {
+            "${params.projName}_contigs.fastg"
+        }
+        else if(filename.equals("Assembly/assembly_graph.gv")) {
+            "${params.projName}_contigs.gv"
+        }
+        else if(filename.equals("Assembly/assembly_info.txt")) {
+            "assembly_info.txt"
+        }
+        else if(filename ==~ /contigs\.fa/) {
+            null //do not publish, but emit for use in downstream process "renameFilterFasta"
+        }
+        else if(filename ==~ /((contig-.*)|(.*contigs\.fa)|(K.*\/final_contigs\.fasta))/) {
+            null //do not publish intermediate contigs, but use downstream
+        }
+        else{
+            filename
+        }
+    }
+    )
+
+    input:
+    path unpaired
+
+    output:
+    path "contigs.log" 
+    path "scaffold*.{fa,fasta}", optional:true //I don't believe this is a normal output of lrasm, but just in case
+    path "contigs.fa", emit:contigs, optional:true
+    path "Assembly/unitig.gfa", optional:true
+    path "Assembly/assembly_graph.gfa", optional:true
+    path "Assembly/assembly_graph.gv", optional:true
+    path "Assembly/assembly_info.txt", optional:true
+    path "{contig-*,*contigs.fa,K*/final_contigs.fasta}", emit: intContigs
+
+    script:
+    def consensus = params.lrasm.numConsensus != null ? "-n $params.lrasm.numConsensus ": ""
+    def preset = params.lrasm.preset != null ? "-x $params.lrasm.preset " : ""
+    def errorCorrection = params.lrasm.ec != null ? "-e " : ""
+    def algorithm = params.lrasm.algorithm != null ? "-a $params.lrasm.algorithm " : ""
+    def minLenOpt = ""
+    if (params.lrasm.algorithm == "miniasm") {
+        minLenOpt = "--ao \'-s $params.lrasm.minLength\' "
+    }
+    else if (params.lrasm.algorithm == "wtdbg2") {
+        minLenOpt = "--wo \'-L $params.lrasm.minLength\' "
+    }
+    def flyeOpt = params.lrasm.algorithm == "metaflye" ? "--fo '--meta' ": ""
+
+    """
+    lrasm -o . -t $params.threads\
+    $preset\
+    $consensus\
+    $errorCorrection\
+    $algorithm\
+    $minLenOpt\
+    $flyeOpt\
+    $unpaired\
+    """
+    //2>/dev/null
+}
+
+process renameFilterFasta {
+    publishDir(
+        path: "$params.outDir/AssemblyBasedAnalysis",
+        mode: 'copy'
+    )
+    input:
+    path contigs
+
+    output:
+    path "*"
+
+    script:
+    def annotation = params.annotation ? "-ann 1" : ""
+    """
+    CONTIG_NUMBER=\$(grep -c '>' ${contigs})
+    
+    renameFilterFasta.pl \
+    -u $contigs\
+    -d .\
+    -filt $params.minContigSize\
+    -maxseq \$CONTIG_NUMBER\
+    -ann_size $params.contigSizeForAnnotation\
+    -n $params.projName\
+    $annotation
+    """
+
+}
+
+process bestIncompleteAssembly {
+    input:
+    val x
+    path intContigs
+
+    when:
+    x == 'EMPTY'
+
+    output:
+    path "bestIntContig/*"
+
+    shell:
+    '''
+    #!/usr/bin/env perl
+    use Cwd;
+    my $dir = getcwd;
+    use Cwd 'abs_path';
+    my @intermediate_contigs = sort { -M $a <=> -M $b} glob("!{intContigs}");
+    my $best_int = $dir . "/" . $intermediate_contigs[0];
+    mkdir bestIntContig;
+    system("cp $best_int ./bestIntContig");
+    '''
+
+}
+
+workflow {
+    "mkdir nf_assets".execute().text
+    "touch nf_assets/NO_FILE".execute().text
+    "touch nf_assets/NO_FILE2".execute().text
+    "touch nf_assets/NO_FILE3".execute().text
+    "touch nf_assets/NO_FILE4".execute().text
+
+    paired_ch = channel.fromPath(params.pairedFiles, relative:true, checkIfExists:true).collect()
+    unpaired_ch = channel.fromPath(params.unpairedFile, relative:true, checkIfExists:true)
+    spades_pb = file(params.spades.pacbio, checkIfExists:true)
+    spades_np = file(params.spades.nanopore, checkIfExists:true)
+    unicycler_lr = file(params.unicycler.longreads, checkIfExists:true)
+
+    if (params.assembler.equalsIgnoreCase("IDBA_UD")) {
+        avg_len_ch = idbaAvgLen(idbaReadFastq(paired_ch, unpaired_ch))
+        (c1,c2) = idbaPrepReads(paired_ch, unpaired_ch)
+        (sp,su,l) = idbaExtractLong(c1,c2.ifEmpty({file("nf_assets/NO_FILE")}))
+        idbaUD(sp.filter{ it.size()>0 }.ifEmpty({file("nf_assets/NO_FILE")}),
+            su.filter{ it.size()>0 }.ifEmpty({file("nf_assets/NO_FILE2")}),
+            l.filter{ it.size()>0 }.ifEmpty({file("nf_assets/NO_FILE3")}),
+            avg_len_ch)
+        
+        bestIncompleteAssembly(idbaUD.out.contigs.ifEmpty('EMPTY'), idbaUD.out.intContigs)
+        renameFilterFasta(idbaUD.out.contigs.concat(bestIncompleteAssembly.out).first())
+
+    }
+    else if (params.assembler.equalsIgnoreCase("SPAdes")) {
+        spades(paired_ch, unpaired_ch, spades_pb, spades_np)
+        
+        bestIncompleteAssembly(spades.out.contigs.ifEmpty('EMPTY'), spades.out.intContigs)
+        renameFilterFasta(spades.out.contigs.concat(bestIncompleteAssembly.out).first())
+    }
+    else if (params.assembler.equalsIgnoreCase("MEGAHIT")) {
+        megahit(paired_ch, unpaired_ch)
+        
+        bestIncompleteAssembly(megahit.out.contigs.ifEmpty('EMPTY'), megahit.out.intContigs)
+        renameFilterFasta(megahit.out.contigs.concat(bestIncompleteAssembly.out).first())
+    }
+    else if (params.assembler.equalsIgnoreCase("UniCycler")) {
+        if (params.unicycler.longreads != "nf_assets/NO_FILE3") {
+            println("Filter long reads with $params.unicycler.minLongReads (bp) cutoff")
+            unicycler(paired_ch,
+                unpaired_ch,
+                unicyclerPrep(unicycler_lr).filter{it.size()>0}.ifEmpty({file("nf_assets/NO_FILE3")}))
+            //unicycler produces no intermediate contigs, we let it error out above rather than try to rescue a failed assembly
+            renameFilterFasta(unicycler.out.contigs)
+        }
+        else {
+            unicycler(paired_ch, unpaired_ch, unicycler_lr)
+            renameFilterFasta(unicycler.out.contigs)
+        }
+    }
+    else if (params.assembler.equalsIgnoreCase("LRASM")) {
+        lrasm(unpaired_ch)
+
+        bestIncompleteAssembly(lrasm.out.contigs.ifEmpty('EMPTY'), lrasm.out.intContigs)
+        renameFilterFasta(lrasm.out.contigs.concat(bestIncompleteAssembly.out).first())
+    }
+    else {
+        error "Invalid assembler: $params.assembler"
+    }
+
+}
\ No newline at end of file
diff --git a/runAssembly/test_files/parameters/idba_assembly.json b/runAssembly/test_files/parameters/idba_assembly.json
new file mode 100644
index 0000000..159b0bc
--- /dev/null
+++ b/runAssembly/test_files/parameters/idba_assembly.json
@@ -0,0 +1,7 @@
+{
+    "assembler":"IDBA_UD",
+    "threads":4,
+    "projName":"test_idba",
+    "pairedFiles":["test_files/Ecoli_10x.1.fastq","test_files/Ecoli_10x.2.fastq"],
+    "outDir": "test_results"
+}
\ No newline at end of file
diff --git a/runAssembly/test_files/parameters/lrasm_assembly.json b/runAssembly/test_files/parameters/lrasm_assembly.json
new file mode 100644
index 0000000..a32a2f4
--- /dev/null
+++ b/runAssembly/test_files/parameters/lrasm_assembly.json
@@ -0,0 +1,10 @@
+{
+    "assembler":"LRASM",
+    "threads":4,
+    "projName":"test_lrasm",
+    "unpairedFile":["test_files/reads.fastq.gz"],
+    "lrasm" : {
+        "ec":true
+    },
+    "outDir": "test_results"
+}
\ No newline at end of file
diff --git a/runAssembly/test_files/parameters/megahit_assembly.json b/runAssembly/test_files/parameters/megahit_assembly.json
new file mode 100644
index 0000000..97415d5
--- /dev/null
+++ b/runAssembly/test_files/parameters/megahit_assembly.json
@@ -0,0 +1,7 @@
+{
+    "assembler":"MEGAHIT",
+    "threads":4,
+    "projName":"test_megahit",
+    "pairedFiles":["test_files/Ecoli_10x.1.fastq","test_files/Ecoli_10x.2.fastq"],
+    "outDir": "test_results"
+}
\ No newline at end of file
diff --git a/runAssembly/test_files/parameters/spades_assembly.json b/runAssembly/test_files/parameters/spades_assembly.json
new file mode 100644
index 0000000..b9aa978
--- /dev/null
+++ b/runAssembly/test_files/parameters/spades_assembly.json
@@ -0,0 +1,7 @@
+{
+    "assembler":"SPAdes",
+    "threads":4,
+    "projName":"test_spades",
+    "pairedFiles":["test_files/Ecoli_10x.1.fastq","test_files/Ecoli_10x.2.fastq"],
+    "outDir": "test_results"
+}
\ No newline at end of file
diff --git a/runAssembly/test_files/parameters/unicycler_assembly.json b/runAssembly/test_files/parameters/unicycler_assembly.json
new file mode 100644
index 0000000..d74f750
--- /dev/null
+++ b/runAssembly/test_files/parameters/unicycler_assembly.json
@@ -0,0 +1,7 @@
+{
+    "assembler":"uNicycleR",
+    "threads":4,
+    "projName":"test_unicycler",
+    "pairedFiles":["test_files/Ecoli_10x.1.fastq","test_files/Ecoli_10x.2.fastq"],
+    "outDir": "test_results"
+}
\ No newline at end of file