diff --git a/asm_annot.nf b/asm_annot.nf
index 051bfba..980963f 100644
--- a/asm_annot.nf
+++ b/asm_annot.nf
@@ -39,7 +39,7 @@ Channel
 
 // run_fastq and run_multiqc are exactly the same as qc_track
 process run_fastqc {
-    publishDir "${params.out_dir}/fastqc", mode: 'copy'
+    publishDir "${params.out_dir}/fastqc", mode: "${params.savemode}"
     tag { pair_id }
     label 'one'
 
@@ -50,13 +50,14 @@ process run_fastqc {
     file "$pair_id" into fastqc_results
 
     """
+    ${preCmd}
     mkdir ${pair_id}
     fastqc -q ${reads} -o ${pair_id} -t $task.cpus
     """
 }
 
 process run_multiqc {
-    publishDir "${params.out_dir}/multiqc", mode: 'copy'
+    publishDir "${params.out_dir}/multiqc", mode: "${params.savemode}"
     tag {"multiqc"}
     label 'one'
 
@@ -67,6 +68,7 @@ process run_multiqc {
     file "multiqc_report.html" into multiqc_report
 
     """
+    ${preCmd}
     multiqc fastqc_output
     """
 }
@@ -98,7 +100,7 @@ process collate_data {
  */
 process run_strip {
 
-    publishDir "${params.out_dir}/bbduk", mode: "copy"
+    publishDir "${params.out_dir}/bbduk", mode: "${params.savemode}"
     tag { pair_id }
 
     input:
@@ -125,7 +127,7 @@ process run_strip {
  * Remove adapter sequences and low quality base pairs with Trimmomatic
  */
 process run_trim {
-    publishDir "${params.out_dir}/bbduk_trimmed", mode: "copy"
+    publishDir "${params.out_dir}/bbduk_trimmed", mode: "${params.savemode}"
     tag { pair_id }
 
     input:
@@ -138,13 +140,13 @@ process run_trim {
     """
     ${preCmd}
     trimmomatic PE -threads $task.cpus -trimlog ${pair_id}_concat_stripped_trimmed.log ${pair_id}*_concat_stripped.fq.gz \
-    -baseout ${pair_id}_trimmed ILLUMINACLIP:${params.adapter_dir}/${params.adapters}:${params.illuminaClipOptions} \
+    -baseout ${pair_id}_trimmed.fq.gz ILLUMINACLIP:${params.adapter_dir}/${params.adapters}:${params.illuminaClipOptions} \
     SLIDINGWINDOW:${params.slidingwindow} \
     LEADING:${params.leading} TRAILING:${params.trailing} \
     MINLEN:${params.minlen} &> ${pair_id}_run.log
-    mv ${pair_id}_trimmed_1P ${pair_id}_R1_concat_stripped_trimmed.fq.gz
-    mv ${pair_id}_trimmed_2P ${pair_id}_R2_concat_stripped_trimmed.fq.gz
-    cat ${pair_id}_trimmed_1U ${pair_id}_trimmed_2U > ${pair_id}_S_concat_stripped_trimmed.fq.gz
+    mv ${pair_id}_trimmed_1P.fq.gz ${pair_id}_R1_concat_stripped_trimmed.fq.gz
+    mv ${pair_id}_trimmed_2P.fq.gz ${pair_id}_R2_concat_stripped_trimmed.fq.gz
+    cat ${pair_id}_trimmed_1U.fq.gz ${pair_id}_trimmed_2U.fq.gz > ${pair_id}_S_concat_stripped_trimmed.fq.gz
     """
 }
 
@@ -153,7 +155,7 @@ process run_trim {
  * Build assembly with SPAdes
  */
 process run_spadesasm {
-     publishDir "${params.out_dir}/spades", mode: "copy"
+     publishDir "${params.out_dir}/spades", mode: "${params.savemode}"
      tag { pair_id }
      label 'longtime'
 
@@ -183,7 +185,7 @@ process run_spadesasm {
  * Map reads to the spades assembly
  */
 process run_bwamem {
-     publishDir "${params.out_dir}/bwamem", mode: "copy"
+     publishDir "${params.out_dir}/bwamem", mode: "${params.savemode}"
      tag { pair_id }
      label 'longtime'
 
@@ -196,6 +198,7 @@ process run_bwamem {
      file("${pair_id}_mapped_sorted.bam.bai") into bwamem_results
 
      """
+     ${preCmd}
      bwa index ${pair_id}_spades_scaffolds.fasta
      bwa mem -t $task.cpus  ${pair_id}_spades_scaffolds.fasta \
      *.fq.gz | samtools sort -o ${pair_id}_mapped_sorted.bam -
@@ -208,7 +211,7 @@ process run_bwamem {
 */
 
 process run_pilon {
-    publishDir "${params.out_dir}/pilon", mode: "copy"
+    publishDir "${params.out_dir}/pilon", mode: "${params.savemode}"
     tag { pair_id }
 
     input:
@@ -222,6 +225,8 @@ process run_pilon {
     file "${pair_id}_pilon_spades.fasta" into asms_for_quast
 
     """
+    ${preCmd}
+    export _JAVA_OPTIONS=$task.javaopts
     pilon --threads $task.cpus --genome ${pair_id}_spades_scaffolds.fasta \
     --bam ${pair_id}_mapped_sorted.bam --output ${pair_id}_pilon_spades \
     --changes --vcfqe &> ${pair_id}_pilon_spades.log
@@ -232,7 +237,7 @@ process run_pilon {
 * Annotation using PROKKA
 */
 process run_prokka {
-    publishDir "${params.out_dir}/prokka", mode: "copy"
+    publishDir "${params.out_dir}/prokka", mode: "${params.savemode}"
     tag { pair_id }
 
     input:
@@ -257,7 +262,7 @@ process run_prokka {
 process quast_eval {
     // The output here is a directory in and of itself
     // thus not creating a new one
-    publishDir "${params.out_dir}/", mode: "copy"
+    publishDir "${params.out_dir}/", mode: "${params.savemode}"
     tag { pair_id }
 
     input:
diff --git a/conf/asm_annot_template.config b/conf/asm_annot_template.config
index 8f83762..be04dc9 100644
--- a/conf/asm_annot_template.config
+++ b/conf/asm_annot_template.config
@@ -22,6 +22,7 @@ params.out_dir = "track_three"
 // General configuration variables
 params.pwd = "$PWD"
 params.help = false
+params.savemode = "copy"
 
 // BBDuk params, has to be absolute paths
 params.stripgenome = "/work/projects/nn9305k/genome_references/genomes/PhiX/PhiX.fasta"
diff --git a/conf/qc_track_template.config b/conf/qc_track_template.config
index 9918b16..2a5c547 100644
--- a/conf/qc_track_template.config
+++ b/conf/qc_track_template.config
@@ -21,6 +21,7 @@ params.out_dir = "track_one"
 // General configuration variables
 params.pwd = "$PWD"
 params.help = false
+params.savemode = "link"
 
 // Raw fastqc results
 params.fastqc = "fastqc"
diff --git a/conf/slurm.config b/conf/slurm.config
index cb82374..0a3d20e 100644
--- a/conf/slurm.config
+++ b/conf/slurm.config
@@ -27,6 +27,9 @@ process {
     cpus = 16
     withLabel: one {cpus = 1}
 
+    //this is mostly for pilon, but can be used elsewhere too
+    javaopts = '-Xmx12G'
+
     time = { 1.h * task.attempt }
     withLabel: longtime {time = { 4.h * task.attempt }}
 }
diff --git a/conf/specific_genes_template.config b/conf/specific_genes_template.config
index 94a3059..5d29c80 100644
--- a/conf/specific_genes_template.config
+++ b/conf/specific_genes_template.config
@@ -15,6 +15,7 @@ params.out_dir = "track_two"
 // General configuration variables
 params.pwd = "$PWD"
 params.help = false
+params.savemode = "copy"
 
 params.threads = 1
 
diff --git a/conf/standard.config b/conf/standard.config
index 5042526..7944644 100644
--- a/conf/standard.config
+++ b/conf/standard.config
@@ -8,4 +8,7 @@ process {
     executor = "local"
     cpus = 1
     maxForks = 2
+    //this is mostly for pilon, but can be used elsewhere too
+    javaopts = ''
+
 }
diff --git a/qc_track.nf b/qc_track.nf
index 59c9f03..1a09a16 100644
--- a/qc_track.nf
+++ b/qc_track.nf
@@ -37,7 +37,7 @@ Channel
 // Second is to send all of through fastqc
 
 process run_fastqc {
-    publishDir "${params.out_dir}/${params.fastqc}", mode: 'copy'
+    publishDir "${params.out_dir}/${params.fastqc}", mode: "${params.savemode}"
     tag {pair_id}
     label 'one'
 
@@ -48,13 +48,14 @@ process run_fastqc {
     file "$pair_id" into fastqc_results
 
     """
+    ${preCmd}
     mkdir ${pair_id}
     fastqc -q ${reads} -o ${pair_id} -t $task.cpus
     """
 }
 
 process run_multiqc {
-    publishDir "${params.out_dir}/multiqc", mode: 'copy'
+    publishDir "${params.out_dir}/multiqc", mode: "${params.savemode}"
     tag {"multiqc"}
     label 'one'
 
@@ -65,6 +66,7 @@ process run_multiqc {
     file "multiqc_report.html" into multiqc_report
 
     """
+    ${preCmd}
     multiqc fastqc_output
     """
 }
diff --git a/specific_genes.nf b/specific_genes.nf
index 4535760..b3c84ff 100644
--- a/specific_genes.nf
+++ b/specific_genes.nf
@@ -66,7 +66,7 @@ process collate_data {
 
 // Download database database
 process run_ariba_mlst_prep {
-    publishDir params.out_dir + "/" + params.mlst_results, mode: 'copy'
+    publishDir "${params.out_dir}" + "/" + "${params.mlst_results}", mode: "${params.savemode}"
     tag {'Dowloading schema'}
     label 'one'
 
@@ -85,7 +85,7 @@ process run_ariba_mlst_prep {
 // Run ariba on each dataset
 
 process run_ariba_mlst_pred {
-    publishDir params.out_dir + "/" + params.mlst_results, mode: 'copy'
+    publishDir "${params.out_dir}" + "/" + "${params.mlst_results}", mode: "${params.savemode}"
     tag {pair_id}
 
     input:
@@ -109,7 +109,7 @@ process run_ariba_mlst_pred {
 
 // Summarize MLST results
 process run_ariba_mlst_summarize {
-    publishDir params.out_dir + "/" + params.mlst_results, mode: 'copy'
+    publishDir "${params.out_dir}" + "/" + "${params.mlst_results}", mode: "${params.savemode}"
     tag {'Summarizing mlst'}
     label 'one'
 
@@ -134,7 +134,7 @@ process run_ariba_mlst_summarize {
 
 //  These three processes are for AMR prediction
 process run_ariba_amr_prep {
-    publishDir params.out_dir + "/" + params.amr_results, mode: 'copy'
+    publishDir "${params.out_dir}" + "/" + "${params.amr_results}", mode: "${params.savemode}"
     tag {'Dowloading AMR data'}
     label 'one'
 
@@ -152,7 +152,7 @@ process run_ariba_amr_prep {
 }
 
 process run_ariba_amr_pred {
-    publishDir params.out_dir + "/" + params.amr_results, mode: 'copy'
+    publishDir "${params.out_dir}" + "/" + "${params.amr_results}", mode: "${params.savemode}"
     tag{pair_id}
 
     input:
@@ -177,7 +177,7 @@ process run_ariba_amr_pred {
 
 // Summarize AMR results
 process run_ariba_amr_summarize {
-    publishDir params.out_dir + "/" + params.amr_results, mode: 'copy'
+    publishDir "${params.out_dir}" + "/" + "${params.amr_results}", mode: "${params.savemode}"
     tag{'Summarizing AMR'}
     label 'one'
 
@@ -198,7 +198,7 @@ process run_ariba_amr_summarize {
 
 //  These three processes are for virulence prediction
 process run_ariba_vir_prep {
-    publishDir params.out_dir + "/" + params.vir_results, mode: 'copy'
+    publishDir "${params.out_dir}" + "/" + "${params.vir_results}", mode: "${params.savemode}"
     tag{'Downloading virulence data'}
     label 'one'
 
@@ -216,7 +216,7 @@ process run_ariba_vir_prep {
 }
 
 process run_ariba_vir_pred {
-    publishDir params.out_dir + "/" + params.vir_results, mode: 'copy'
+    publishDir "${params.out_dir}" + "/" + "${params.vir_results}", mode: "${params.savemode}"
     tag{pair_id}
 
     input:
@@ -241,7 +241,7 @@ process run_ariba_vir_pred {
 
 // Summarize virulence results
 process run_ariba_vir_summarize {
-    publishDir params.out_dir + "/" + params.vir_results, mode: 'copy'
+    publishDir "${params.out_dir}" + "/" + "${params.vir_results}", mode: "${params.savemode}"
     tag{'Summarizing virulence'}
     label 'one'