diff --git a/bin/get_fasta_largest_isoform.TrinityMS.pl b/bin/get_fasta_largest_isoform.TrinityMS.pl
index 2269273..fd57b3a 100755
--- a/bin/get_fasta_largest_isoform.TrinityMS.pl
+++ b/bin/get_fasta_largest_isoform.TrinityMS.pl
@@ -4,9 +4,14 @@
 use FindBin;
 use lib ("$FindBin::RealBin/PerlLib");
 use Getopt::Std;
+use Bio::SeqIO;
 
+# This script reads in a fasta file and produces the longest transcript for each gene (if present in ensembl, trinity or basic headers are present). 
+# This is to stop multiple isoforms of the same gene going through. 
+# If you wish all genes/isoforms to go through, use "basic"
+# It then prints out the longest isoform for each gene, or all genes. 
 
-die "Please specify (1)fasta file (2) nucl type (ensembl, trinity)\n" unless(@ARGV==2);
+die "Please specify (1)fasta file (2) nucl type (ensembl, trinity, basic)\n" unless(@ARGV==2);
 
 my $fastafile = $ARGV[0];
 my $nucl_type = $ARGV[1];
@@ -19,7 +24,6 @@
 if ($nucl_type eq "trinity"){
 
 
-use Bio::SeqIO;
 my $seqio = Bio::SeqIO->new(-file => "$fastafile", '-format' => 'Fasta');
 my %fastadictionary=();
 my @headersplit=();
@@ -49,7 +53,7 @@
 
 foreach my $key ( sort keys %fastadictionary){
 	if ($fastadictionary{$key} eq "Sequenceunavailable"){
-
+		#Do nothing
 	}
 	else{
 		print $outhandle ">$key\n$fastadictionary{$key}\n";
@@ -61,7 +65,6 @@
 
 if ($nucl_type eq "ensembl"){
 	
-use Bio::SeqIO;
 my $seqio = Bio::SeqIO->new(-file => "$fastafile", '-format' => 'Fasta');
 my %fastadictionary=();
 my @headersplit=();
@@ -87,20 +90,53 @@
 	
 }
 
-print "Now print new fasta with one main protein per gene.\n";
+#print "Now print new fasta with one main protein per gene.\n";
 
 foreach my $key ( sort keys %fastadictionary){
 	if ($fastadictionary{$key} eq "Sequenceunavailable"){
-
+		#Do nothing
 	}
 	else{
 		print $outhandle ">$key\n$fastadictionary{$key}\n";
-	}
-	
+	}	
+}
+
+}
+
+
+if ($nucl_type eq "basic"){
+
+my $seqio = Bio::SeqIO->new(-file => "$fastafile", '-format' => 'Fasta');
+my %fastadictionary=();
+my @headersplit=();
+while (my $seq = $seqio->next_seq){ ## selects one sequence at a time
+        ## set variables for THIS sequence
+        my $id = $seq->display_id;
+        my $string = $seq->seq;
+        my $len=length($string);
+        if ($fastadictionary{$id}){
+                my $len_old=length($fastadictionary{$id});
+                if ($len >= $len_old){
+                        $fastadictionary{$id}=$string;
+                }
+        }
+	else{
+             	$fastadictionary{$id}=$string;
+        }
 }
 
+print "Now print new fasta with one main protein per gene.\n";
+
+foreach my $key ( sort keys %fastadictionary){
+        if ($fastadictionary{$key} eq "Sequenceunavailable"){
+                #Do nothing
+        }
+        else{
+                print $outhandle ">$key\n$fastadictionary{$key}\n";
+        }
 }
 
+}
 
 print "Finished:  input lines, output lines\n";
 
diff --git a/bin/get_fasta_largest_isoform.ensembl.pl b/bin/get_fasta_largest_isoform.ensembl.pl
deleted file mode 100755
index f4a3905..0000000
--- a/bin/get_fasta_largest_isoform.ensembl.pl
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/usr/bin/env perl
-use warnings;
-use strict;
-use FindBin;
-use lib ("$FindBin::RealBin/PerlLib");
-use Getopt::Std;
-
-
-die "Please specify (1)fasta file\n" unless(@ARGV==1);
-
-my $fastafile = $ARGV[0];
-my $outfile="$fastafile\.largestIsoform";
-
-#open(my $fastahandle, "<", $fastafile)   or die "Could not open $fastafile \n"; no need to open here for bioperl
-#open(my $fastafile, "<", $fastafile)   or die "Could not open $fastafile \n";
-open(my $outhandle, ">", $outfile)   or die "Could not open $outfile \n";
-
-
-use Bio::SeqIO;
-my $seqio = Bio::SeqIO->new(-file => "$fastafile", '-format' => 'Fasta');
-my %fastadictionary=();
-my @headersplit=();
-while (my $seq = $seqio->next_seq){ ## selects one sequence at a time
-   	## set variables for THIS sequence
-        my $id = $seq->display_id;
-	my $string = $seq->seq;
-	my @split=split(/\:/, $id);
-	#my @spl2=split("\_", $split[0]);
-	#my $waste=pop @spl2;
-	my $new_id=$split[1];
-	my $len=length($string);
-	#print "length = $len\n";
-	if ($fastadictionary{$new_id}){
-		my $len_old=length($fastadictionary{$new_id});
-		if ($len >= $len_old){
-			$fastadictionary{$new_id}=$string;
-		}
-	}
-	else{
-		$fastadictionary{$new_id}=$string;
-	}
-	
-}
-
-print "Now print new fasta with one main protein per gene.\n";
-
-foreach my $key ( sort keys %fastadictionary){
-	if ($fastadictionary{$key} eq "Sequenceunavailable"){
-
-	}
-	else{
-		print $outhandle ">$key\n$fastadictionary{$key}\n";
-	}
-	
-}
-
-print "Finished:  input lines, output lines\n";
-
diff --git a/conf/base.config b/conf/base.config
new file mode 100644
index 0000000..5d6af80
--- /dev/null
+++ b/conf/base.config
@@ -0,0 +1,67 @@
+// Setting default labels with associated resource allocation
+process {
+
+    // Default resources are same as single label for any unlabelled processes that may be added
+    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
+    memory = { check_max( 2.GB * task.attempt, 'memory' ) }
+    time   = { check_max( 1.h  * task.attempt, 'time'   ) }
+
+    // If error is due to timeout or exceeding resource limits then retry
+    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    maxRetries    = 1
+    // Do not allow any errors when retrying
+    maxErrors     = '-1'
+
+    withLabel:process_single {
+        cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
+        memory = { check_max( 2.GB * task.attempt, 'memory' ) }
+        time   = { check_max( 1.h  * task.attempt, 'time'   ) }
+    }
+    withLabel:process_low {
+        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 4.GB  * task.attempt, 'memory'  ) }
+        time   = { check_max( 2.h   * task.attempt, 'time'    ) }
+    }
+    withLabel:process_medium {
+        cpus   = { check_max( 4     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }
+        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+    }
+    withLabel:process_high {
+        cpus   = { check_max( 8     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+    }
+    withLabel:process_long {
+        time   = { check_max( 24.h  * task.attempt, 'time'    ) }
+    }
+    withLabel:process_high_memory {
+        memory = { check_max( 64.GB * task.attempt, 'memory' ) }
+    }
+    withLabel:process_med_memory {
+        memory = { check_max( 20.GB * task.attempt, 'memory' ) }
+    }
+    withLabel:download_nr {
+        memory = 12.GB
+        cpus = 2
+        time = 24.h
+    }
+    withLabel:blastdb {
+        memory = 40.GB
+        cpus = 4
+        time = 8.h
+    }
+    withLabel:blast {
+        memory = 40.GB
+        cpus = 4
+        time = 8.h
+    }
+    withLabel:error_ignore {
+        errorStrategy = 'ignore'
+    }
+    withLabel:error_retry {
+        errorStrategy = 'retry'
+        maxRetries    = 2
+    }
+
+}
diff --git a/main.firstattempt.nf b/main.firstattempt.nf
deleted file mode 100755
index 977b37a..0000000
--- a/main.firstattempt.nf
+++ /dev/null
@@ -1,87 +0,0 @@
-/*
- * Copyright (c) 2021
- */
- 
-
- /*
- * Authors:
- * - Chris Wyatt <chris.wyatt@seqera.io>
- */
-
-params.proteins= false
-params.nucleotide = false
-params.nucl_type = "ensembl"
-params.predownloaded= false
-params.numhits = 1
-params.outdir = "results"
-params.names = false
-params.nodes = false
-params.level = "family"
-params.sensitivity= "fast"
-
-log.info """\
- ===================================
- proteins                             : ${params.proteins}
- nucleotides                          : ${params.nucleotide}
- out directory                        : ${params.outdir}
- """
-
-//================================================================================
-// Include modules
-//================================================================================
-
-include { DOWNLOAD } from './modules/download.nf'
-include { MAKE_DB } from './modules/make_blast_db.nf'
-include { DIAMOND_BLAST } from './modules/diamond_blast.nf'
-include { PLOT_PIE } from './modules/plot_taxonomy_pie.nf'
-include { T_DECODER } from './modules/transdecoder.nf'
-
-
-workflow {
-	if ( params.proteins ){
-	    	input_target_proteins = channel
-	    	.fromPath(params.proteins)
-	    	.splitCsv()
-    		.ifEmpty { error "Cannot find the list of protein files: ${params.proteins}" }
-	}
-	else if( params.nucleotide ){
-		input_target_nucleotide = channel
-	        .fromPath(params.nucleotide)
-		.splitCsv()
-		.ifEmpty { error "Cannot find the list of nucleotide files: ${params.nucleotide}" }
-		.view()
-		T_DECODER ( input_target_nucleotide )
-		T_DECODER.out.protein.set{ input_target_proteins }
-	}
-	else{
-		println "You have not set the input protein or nucleotide option\n"
-	}
-
-
-	if ( !params.predownloaded ){
-		// If not predownloaded then wget all from NCBI.
-		println "Downloading a new nr database with taxonomy information\n"
-		DOWNLOAD ()
-		MAKE_DB ( DOWNLOAD.out.database , DOWNLOAD.out.accession2taxid , DOWNLOAD.out.tax_nodes , DOWNLOAD.out.tax_names )
-		DIAMOND_BLAST ( input_target_proteins , MAKE_DB.out.blast_database )
-		PLOT_PIE ( DOWNLOAD.out.tax_nodes , DOWNLOAD.out.tax_names , DIAMOND_BLAST.out.blast_hits )
-		
-	}
-	else{
-		//input_database = channel
-		//	.fromPath(params.predownloaded)
-		//	.ifEmpty { error "Cannot find the blast database : ${params.predownloaded}" }
-		//input_names = channel
-                //        .fromPath(params.names)
-                //        .ifEmpty { error "Cannot find the blast database : ${params.names}" }
-		//input_nodes = channel
-                //        .fromPath(params.nodes)
-                //        .ifEmpty { error "Cannot find the blast database : ${params.nodes}" }
-		DIAMOND_BLAST ( input_target_proteins , params.predownloaded )
-		PLOT_PIE ( params.nodes , params.names , DIAMOND_BLAST.out.blast_hits )
-	}
-}
-
-workflow.onComplete {
-	println ( workflow.success ? "\nDone! Open your report in your browser --> $params.outdir/report.html (if you added -with-report flag)\n" : "Hmmm .. something went wrong" )
-}
diff --git a/main.nf b/main.nf
index cd88022..f632b3c 100755
--- a/main.nf
+++ b/main.nf
@@ -1,8 +1,9 @@
 /*
  * Copyright (c) 2021
  */
+ 
 
-/*
+ /*
  * Authors:
  * - Chris Wyatt <chris.wyatt@seqera.io>
  */
@@ -10,22 +11,20 @@
 params.proteins= false
 params.nucleotide = false
 params.predownloaded= false
+params.numhits = 1
 params.outdir = "results"
 params.names = false
 params.nodes = false
-params.numhits = null
-params.tophits = null
 params.level = "family"
-params.sensitivity = "fast"
-params.horizontal = false
-params.xml = false
+params.sensitivity= "fast"
+params.nucl_type = "trinity"
 
 log.info """\
-===================================
-proteins                             : ${params.proteins}
-nucleotides                          : ${params.nucleotide}
-out directory                        : ${params.outdir}
-"""
+ ===================================
+ proteins                             : ${params.proteins}
+ nucleotides                          : ${params.nucleotide}
+ out directory                        : ${params.outdir}
+ """
 
 //================================================================================
 // Include modules
@@ -33,55 +32,22 @@ out directory                        : ${params.outdir}
 
 include { DOWNLOAD } from './modules/download.nf'
 include { MAKE_DB } from './modules/make_blast_db.nf'
+include { DIAMOND_BLAST } from './modules/diamond_blast.nf'
 include { PLOT_PIE } from './modules/plot_taxonomy_pie.nf'
 include { T_DECODER } from './modules/transdecoder.nf'
-include { DIAMOND_BLAST } from './modules/diamond_blast.nf'
-include { DIAMOND_HORIZONTAL } from './modules/diamond_horizontal.nf'
-include { DIAMOND_XML } from './modules/diamond_xml.nf'
-
-workflow {
-	input_database = Channel.empty()
-	input_names    = Channel.empty()
-	input_nodes    = Channel.empty()
-
-	if ( !params.predownloaded ){
-		// If not predownloaded then wget all from NCBI.
-		println "Downloading a new nr database with taxonomy information\n"
-		DOWNLOAD ()
-		MAKE_DB ( DOWNLOAD.out.database , DOWNLOAD.out.accession2taxid , DOWNLOAD.out.tax_nodes , DOWNLOAD.out.tax_names )
-		MAKE_DB.out.blast_database.first().set{ input_database }
-		DOWNLOAD.out.tax_names.first().set{ input_names }
-		DOWNLOAD.out.tax_nodes.first().set{ input_nodes }
-	}
-	else{
-		input_database = channel
-			.fromPath(params.predownloaded)
-			.ifEmpty { error "Cannot find the blast database : ${params.predownloaded}" }
-			.first()
-		input_names = channel
-            .fromPath(params.names)
-            .ifEmpty { error "Cannot find the blast database : ${params.names}" }
-			.first()
-		input_nodes = channel
-            .fromPath(params.nodes)
-            .ifEmpty { error "Cannot find the blast database : ${params.nodes}" }
-            .first()
-	}
 
-	input_target_proteins = Channel.empty()
 
+workflow {
 	if ( params.proteins ){
 		input_target_proteins = channel
 		.fromPath(params.proteins)
-		.splitCsv()
 		.ifEmpty { error "Cannot find the list of protein files: ${params.proteins}" }
 	}
 	else if( params.nucleotide ){
 		input_target_nucleotide = channel
                 .fromPath(params.nucleotide)
-		.splitCsv()
                 .ifEmpty { error "Cannot find the list of protein files: ${params.nucleotide}" }
-		T_DECODER ( input_target_nucleotide )
+		T_DECODER ( input_target_nucleotide , params.nucl_type )
 		T_DECODER.out.protein.set{ input_target_proteins }
 	}
 	else{
@@ -89,16 +55,30 @@ workflow {
 	}
 
 
-	DIAMOND_BLAST ( input_target_proteins , input_database )
-	
-	PLOT_PIE ( input_nodes , input_names , DIAMOND_BLAST.out.blast_hits )
-
-	//if ( params.horizontal ){
-	//	DIAMOND_HORIZONTAL ( input_target_proteins , input_database )
-	//}
-
-	if ( params.xml ){
-		DIAMOND_XML ( input_target_proteins , input_database )
+	if ( !params.predownloaded ){
+		// If not predownloaded then wget all from NCBI.
+		println "Downloading a new nr database with taxonomy information\n"
+		DOWNLOAD ()
+		MAKE_DB ( DOWNLOAD.out.database , DOWNLOAD.out.accession2taxid , DOWNLOAD.out.tax_nodes , DOWNLOAD.out.tax_names )
+		DIAMOND_BLAST ( input_target_proteins , MAKE_DB.out.blast_database )
+		PLOT_PIE ( DOWNLOAD.out.tax_names , DOWNLOAD.out.tax_nodes , DIAMOND_BLAST.out.blast_hits )
+		
+	}
+	else{
+		input_database = channel
+			.fromPath(params.predownloaded)
+			.ifEmpty { error "Cannot find the blast database : ${params.predownloaded}" }
+			.first()	
+		input_names = channel
+                        .fromPath(params.names)
+                        .ifEmpty { error "Cannot find the blast database : ${params.names}" }
+			.first()
+		input_nodes = channel
+                        .fromPath(params.nodes)
+                        .ifEmpty { error "Cannot find the blast database : ${params.nodes}" }
+			.first()
+		DIAMOND_BLAST ( input_target_proteins , input_database )
+		PLOT_PIE ( input_nodes , input_names , DIAMOND_BLAST.out.blast_hits )
 	}
 }
 
diff --git a/main.secondattempt.nf b/main.secondattempt.nf
deleted file mode 100755
index d8a815a..0000000
--- a/main.secondattempt.nf
+++ /dev/null
@@ -1,86 +0,0 @@
-/*
- * Copyright (c) 2021
- */
- 
-
- /*
- * Authors:
- * - Chris Wyatt <chris.wyatt@seqera.io>
- */
-
-params.proteins= false
-params.nucleotide = false
-params.predownloaded= false
-params.numhits = 1
-params.outdir = "results"
-params.names = false
-params.nodes = false
-params.level = "family"
-params.sensitivity= "fast"
-
-log.info """\
- ===================================
- proteins                             : ${params.proteins}
- nucleotides                          : ${params.nucleotide}
- out directory                        : ${params.outdir}
- """
-
-//================================================================================
-// Include modules
-//================================================================================
-
-include { DOWNLOAD } from './modules/download.nf'
-include { MAKE_DB } from './modules/make_blast_db.nf'
-include { DIAMOND_BLAST } from './modules/diamond_blast.nf'
-include { PLOT_PIE } from './modules/plot_taxonomy_pie.nf'
-include { T_DECODER } from './modules/transdecoder.nf'
-
-
-workflow {
-	if ( params.proteins ){
-        	input_target_proteins = channel
-        	.fromPath(params.proteins)
-        	.ifEmpty { error "Cannot find the list of protein files: ${params.proteins}" }
-	}
-	else if( params.nucleotide ){
-		input_target_nucleotide = channel
-                .fromPath(params.nucleotide)
-                .ifEmpty { error "Cannot find the list of protein files: ${params.nucleotide}" }
-		T_DECODER ( input_target_nucleotide )
-		T_DECODER.out.protein.set{ input_target_proteins }
-	}
-	else{
-		println "You have not set the input protein or nucleotide option\n"
-	}
-
-
-	if ( !params.predownloaded ){
-		// If not predownloaded then wget all from NCBI.
-		println "Downloading a new nr database with taxonomy information\n"
-		DOWNLOAD ()
-		MAKE_DB ( DOWNLOAD.out.database , DOWNLOAD.out.accession2taxid , DOWNLOAD.out.tax_nodes , DOWNLOAD.out.tax_names )
-		DIAMOND_BLAST ( input_target_proteins , MAKE_DB.out.blast_database )
-		PLOT_PIE ( DOWNLOAD.out.tax_names , DOWNLOAD.out.tax_nodes , DIAMOND_BLAST.out.blast_hits )
-		
-	}
-	else{
-		input_database = channel
-			.fromPath(params.predownloaded)
-			.ifEmpty { error "Cannot find the blast database : ${params.predownloaded}" }
-			.first()	
-		input_names = channel
-                        .fromPath(params.names)
-                        .ifEmpty { error "Cannot find the blast database : ${params.names}" }
-			.first()
-		input_nodes = channel
-                        .fromPath(params.nodes)
-                        .ifEmpty { error "Cannot find the blast database : ${params.nodes}" }
-			.first()
-		DIAMOND_BLAST ( input_target_proteins , input_database )
-		PLOT_PIE ( input_nodes , input_names , DIAMOND_BLAST.out.blast_hits )
-	}
-}
-
-workflow.onComplete {
-	println ( workflow.success ? "\nDone! Open your report in your browser --> $params.outdir/report.html (if you added -with-report flag)\n" : "Hmmm .. something went wrong" )
-}
diff --git a/modules/diamond_blast.nf b/modules/diamond_blast.nf
index 8b25e72..bfae37b 100755
--- a/modules/diamond_blast.nf
+++ b/modules/diamond_blast.nf
@@ -1,7 +1,7 @@
 process DIAMOND_BLAST {
     label 'blast'
+    container = 'chriswyatt/diamond'
     publishDir "$params.outdir/Blast_results/", mode:'copy'
-    //stageInMode 'copy'
     
     input:
         path proteins
diff --git a/modules/diamond_horizontal.nf b/modules/diamond_horizontal.nf
index 862cd4b..9b08d83 100755
--- a/modules/diamond_horizontal.nf
+++ b/modules/diamond_horizontal.nf
@@ -1,7 +1,7 @@
 process DIAMOND_HORIZONTAL {
     label 'blast'
+    container = 'chriswyatt/diamond'
     publishDir "$params.outdir/Blast_results/", mode:'copy'
-    //stageInMode 'copy'
     
     input:
         path proteins
diff --git a/modules/diamond_xml.nf b/modules/diamond_xml.nf
index ae16ae6..e80c0fb 100755
--- a/modules/diamond_xml.nf
+++ b/modules/diamond_xml.nf
@@ -1,7 +1,7 @@
 process DIAMOND_XML {
     label 'blast'
+    container = 'chriswyatt/diamond'
     publishDir "$params.outdir/Blast_results/", mode:'copy'
-    //stageInMode 'copy'
     
     input:
         path proteins
diff --git a/modules/download.nf b/modules/download.nf
index 05236a4..3b51266 100755
--- a/modules/download.nf
+++ b/modules/download.nf
@@ -1,11 +1,13 @@
 process DOWNLOAD {
-    label 'download'
-               
+    label 'download_nr'
+    time 24.h
+    container 'quay.io/ecoflowucl/ncbi_download:v16.1.2-arm64'
     output:
         path("nr.gz") , emit: database
-	path("prot.accession2taxid.FULL") , emit: accession2taxid
+        path("prot.accession2taxid.FULL") , emit: accession2taxid
         path("nodes.dmp") , emit: tax_nodes
         path("names.dmp") , emit: tax_names
+
     script:
     """
     wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz
diff --git a/modules/make_blast_db.nf b/modules/make_blast_db.nf
index e44f2d7..e2e83d4 100755
--- a/modules/make_blast_db.nf
+++ b/modules/make_blast_db.nf
@@ -1,6 +1,7 @@
 process MAKE_DB {
     label 'blastdb'
-    //stageInMode 'copy'
+    container = 'chriswyatt/diamond'
+
     input:
         path nr_gz
         path prot_accession2taxid
diff --git a/modules/plot_taxonomy_pie.nf b/modules/plot_taxonomy_pie.nf
index e0ab058..e7529d8 100755
--- a/modules/plot_taxonomy_pie.nf
+++ b/modules/plot_taxonomy_pie.nf
@@ -1,5 +1,6 @@
 process PLOT_PIE {
     label 'perl_pie'
+    container = 'chriswyatt/perl_r_e1071'
     publishDir "$params.outdir/Blast_results/", mode:'copy', pattern: '*top.tsv'
     publishDir "$params.outdir/Taxo_figure/", mode:'copy', pattern: '*.pdf'
     publishDir "$params.outdir/Taxo_summary/", mode:'copy', pattern: '*_summary.tsv'
diff --git a/modules/transdecoder.nf b/modules/transdecoder.nf
index 18b990b..fc41fcb 100755
--- a/modules/transdecoder.nf
+++ b/modules/transdecoder.nf
@@ -1,16 +1,18 @@
 process T_DECODER {
-    label 'transdecoder'
+    label 'process_low'
     publishDir "$params.outdir/Prot/", mode:'copy', pattern: '*.prot.fa'
+    container = 'chriswyatt/transdecoder'
 
     input:
-	path fasta_file
-               
+        path fasta_file
+        val type
+
     output:
         path("${fasta_file}.prot.fa") , emit: protein
 
     script:
     """
-	get_fasta_largest_isoform.TrinityMS.pl $fasta_file $params.nucl_type
+	get_fasta_largest_isoform.TrinityMS.pl $fasta_file $type
 	TransDecoder.LongOrfs -t ${fasta_file}.largestIsoform --output_dir Output
 	cp Output/longest_orfs.pep ${fasta_file}.prot.fa
     """
diff --git a/myriad.config b/myriad.config
new file mode 100644
index 0000000..9e63200
--- /dev/null
+++ b/myriad.config
@@ -0,0 +1,15 @@
+executor {
+  name = 'sge'
+}
+
+apptainer.runOptions = "-B ${HOME},${PWD}"
+
+process {
+
+    //NEED TO SET PARALLEL ENVIRONMENT TO SMP SO MULTIPLE CPUS CAN BE SUBMITTED
+    penv = 'smp'
+
+    //PROVIDE EXTRA PARAMETERS AS CLUSTER OPTIONS
+    clusterOptions = { "-S /bin/bash -l mem=${task.memory.mega}M" }
+    //clusterOptions = { "-S /bin/bash-l h_rt=${task.time.toHours()}h" }
+}
diff --git a/nextflow.config b/nextflow.config
index 509bce0..4d1e359 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -15,4 +15,55 @@ profiles {
   cscluster {
     includeConfig 'conf/cscluster.config'
   }
+  apptainer {
+    apptainer.enabled        = true
+    // Set where singularity cached images are saved
+    apptainer.cacheDir       = "apptainer/cachedir"
+    // set registry to quay.io
+    //apptainer.registry       = "quay.io"
+    // Ensure other container engines are unset
+    docker.enabled           = false
+    singularity.enabled      = false
+  }
+}
+
+// Load base.config by default for all pipelines
+includeConfig 'conf/base.config'
+
+
+// Function to ensure that resource requirements don't go beyond a maximum limit
+def check_max(obj, type) {
+    if (type == 'memory') {
+        try {
+            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
+                return params.max_memory as nextflow.util.MemoryUnit
+            else
+                return obj
+        } catch (all) {
+            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
+            return obj
+        }
+    } else if (type == 'time') {
+        try {
+            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
+                return params.max_time as nextflow.util.Duration
+            else
+                return obj
+        } catch (all) {
+            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
+            return obj
+        }
+    } else if (type == 'cpus') {
+        try {
+            return Math.min( obj, params.max_cpus as int )
+        } catch (all) {
+            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
+            return obj
+        }
+    }
+}
+
+params {
+    max_cpus = 4 // or any valid integer
+    max_memory = '32 GB'
 }