diff --git a/.github/workflows/github_actions.config b/.github/workflows/github_actions.config
index d79f3021..d5ec9499 100644
--- a/.github/workflows/github_actions.config
+++ b/.github/workflows/github_actions.config
@@ -1,4 +1,4 @@
-includeConfig '/home/runner/work/Cecret/Cecret/configs/cecret_config_template.config'
+params.vadr = false
 
 process {
   withName:ivar_consensus{
diff --git a/.github/workflows/test_primers.yml b/.github/workflows/test_primers.yml
index c913614b..d601785f 100644
--- a/.github/workflows/test_primers.yml
+++ b/.github/workflows/test_primers.yml
@@ -19,8 +19,7 @@ jobs:
                 'ncov_V4', 
                 'ncov_V4.1', 
                 'ncov_V5.3.2', 
-                'mpx_primalseq', 
-                'mpx_idt'
+                'mpx_primalseq'
                 ]
 
     steps:
diff --git a/.github/workflows/test_profile.yml b/.github/workflows/test_profile.yml
index 19e2e8bc..13628f11 100644
--- a/.github/workflows/test_profile.yml
+++ b/.github/workflows/test_profile.yml
@@ -24,7 +24,7 @@ jobs:
           
       - name: Run Cecret
         run: |
-          nextflow run . -profile docker,test -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 --vadr false
+          nextflow run . -profile docker,test -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 --vadr false --aci false --freyja false
 
           ls cecret*
             
diff --git a/.github/workflows/test_profile1.yml b/.github/workflows/test_profile1.yml
index fcee51b1..2f57d30d 100644
--- a/.github/workflows/test_profile1.yml
+++ b/.github/workflows/test_profile1.yml
@@ -24,7 +24,7 @@ jobs:
           
       - name: Run Cecret
         run: |
-          nextflow run . -profile docker,test1 -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 --vadr false
+          nextflow run . -profile docker,test1 -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 --vadr false --aci false --freyja false
 
           ls cecret*
             
diff --git a/.github/workflows/test_profile2.yml b/.github/workflows/test_profile2.yml
index b541c60f..7c035359 100644
--- a/.github/workflows/test_profile2.yml
+++ b/.github/workflows/test_profile2.yml
@@ -24,7 +24,7 @@ jobs:
           
       - name: Run Cecret
         run: |
-          nextflow run . -profile docker,test2 -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 --vadr false
+          nextflow run . -profile docker,test2 -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 --vadr false --aci false --freyja false
 
           ls cecret*
             
diff --git a/bin/.tests.notower.sh b/bin/.tests.notower.sh
deleted file mode 100755
index 8482b4cf..00000000
--- a/bin/.tests.notower.sh
+++ /dev/null
@@ -1,99 +0,0 @@
-#/bin/bash
-#nextflow ~/sandbox/Cecret/Cecret.nf -profile singularity --reads /home/eriny/sandbox/test_files/cecret/reads --outdir tests -with-tower -resume
-
-test=$1
-
-if [ -z "$test" ]; then test="small" ; fi
-
-if [ "$test" == "small" ]
-then
-  options=("reads" "single_reads" "fastas")
-
-  for option in ${options[@]}
-  do
-    # defaults
-    nextflow ~/sandbox/Cecret/Cecret.nf \
-      -profile singularity,artic_V3 \
-      --$option /home/eriny/sandbox/test_files/cecret/$option \
-      --outdir singularity_defaults_$option
-
-    # removed test for bamsnap and rename because of lack of interest
-    # attempted bcftools and filter
-    nextflow ~/sandbox/Cecret/Cecret.nf \
-      -profile singularity,artic_V3 \
-      --$option /home/eriny/sandbox/test_files/cecret/$option \
-      --outdir all_on_$option \
-      --bcftools_variants true \
-      --filter true \
-      -resume
-
-    # removing primer trimming
-    nextflow ~/sandbox/Cecret/Cecret.nf \
-      -profile singularity,artic_V3 \
-      --$option /home/eriny/sandbox/test_files/cecret/$option \
-      --outdir nontrimmed_$option \
-      --trimmer 'none' \
-      -resume
-
-    # changing the cleaner, aligner, and trimmer
-    nextflow ~/sandbox/Cecret/Cecret.nf \
-      -profile singularity,artic_V3 \
-      --$option /home/eriny/sandbox/test_files/cecret/$option \
-      --outdir toggled_$option \
-      --cleaner 'fastp' \
-      --trimmer 'samtools' \
-      --aligner 'minimap2' \
-      -resume
-
-    # with UPHL's config
-    nextflow ~/sandbox/Cecret/Cecret.nf \
-      -profile uphl,artic_V3 \
-      --$option /home/eriny/sandbox/test_files/cecret/$option \
-      --outdir uphl_$option \
-      -resume
-  done
-
-  # multifasta
-  nextflow ~/sandbox/Cecret/Cecret.nf \
-    -profile singularity,artic_V3 \
-    --reads /home/eriny/sandbox/test_files/cecret/reads \
-    --single-reads /home/eriny/sandbox/test_files/cecret/single-reads \
-    --fastas /home/eriny/sandbox/test_files/cecret/fastas \
-    --multifastas /home/eriny/sandbox/test_files/cecret/multifasta \
-    --outdir kitchen_sink
-
-  # empty
-  nextflow ~/sandbox/Cecret/Cecret.nf \
-    -profile singularity,artic_V3 \
-    --reads doesntexit \
-    --single-reads willnotexist \
-    --fastas shouldntexit \
-    --outdir empty
-
-else
-  # CDC's test data with relatedness
-  nextflow ~/sandbox/Cecret/Cecret.nf \
-    -profile singularity,artic_V3 \
-    --reads /home/eriny/sandbox/sars-cov-2-datasets/reads \
-    --outdir default_datasets \
-    --relatedness true
-
-  nextflow ~/sandbox/Cecret/Cecret.nf \
-    -profile uphl,artic_V3 \
-    --reads /home/eriny/sandbox/sars-cov-2-datasets/reads \
-    --outdir uphl_datasets \
-    -resume \
-    --relatedness true
-
-  # CDC's test data with relatedness using nextalign
-  nextflow ~/sandbox/Cecret/Cecret.nf \
-    -profile singularity,artic_V3 \
-    --reads /home/eriny/sandbox/sars-cov-2-datasets/reads \
-    --outdir toggled_datasets \
-    --cleaner 'fastp' \
-    --trimmer 'samtools' \
-    --aligner 'minimap2' \
-    --relatedness true \
-    --msa 'nextalign' \
-    -resume
-fi
diff --git a/bin/.tests.sh b/bin/.tests.sh
index a3091390..5019c1ef 100755
--- a/bin/.tests.sh
+++ b/bin/.tests.sh
@@ -3,6 +3,8 @@
 # nextflow run ~/sandbox/Cecret -profile singularity,mpx --reads /home/eriny/sandbox/test_files/cecret/mpx --outdir tests --cleaner 'fastp' -with-tower -resume
 # nextflow run ~/sandbox/Cecret -profile singularity --nanopore /home/eriny/sandbox/test_files/cecret/nanopore --outdir tests -with-tower -resume
 
+echo "usage : bash .test.sh {small,primers,else}"
+
 test=$1
 
 if [ -z "$test" ]; then test="small" ; fi
@@ -36,6 +38,7 @@ then
       -profile singularity,artic_V3 \
       --$option /home/eriny/sandbox/test_files/cecret/$option \
       --outdir singularity_defaults_$option \
+      -resume \
       -with-tower
 
     # removed test for bamsnap and rename because of lack of interest
@@ -96,6 +99,83 @@ then
     --outdir empty  \
     -with-tower
 
+elif [ "$test" == "primers" ]
+then
+
+  nanopore_primers=("midnight_idt_V1" "midnight_ont_V1" "midnight_ont_V2" "midnight_ont_V3")
+  for primer in ${nanopore_primers[@]}
+  do
+    nextflow run ~/sandbox/Cecret \
+      -profile singularity \
+      --nanopore /home/eriny/sandbox/test_files/cecret/nanopore \
+      --outdir primer_${primer}_artic \
+      --primer_set $primer \
+      --bcftools_variants false \
+      --fastqc false \
+      --ivar_variants false \
+      --samtools_stats false \
+      --samtools_coverage false \
+      --samtools_depth false \
+      --nextclade false \
+      --pangolin false \
+      --freyja false \
+      --vadr false \
+      -resume \
+      -with-tower
+  done
+
+  trimmers=("samtools" "ivar")
+  for trimmer in ${trimmers[@]}
+  do
+    illumina_primers=("ncov_V3" "ncov_V4" "ncov_V4.1" "ncov_V5.3.2")
+    for primer in ${illumina_primers[@]}
+    do
+      nextflow run ~/sandbox/Cecret \
+        -profile singularity \
+        --reads /home/eriny/sandbox/test_files/cecret/reads \
+        --outdir primer_${primer}_${trimmer} \
+        --trimmer $trimmer \
+        --cleaner 'fastp' \
+        --primer_set $primer \
+        --bcftools_variants false \
+        --fastqc false \
+        --ivar_variants false \
+        --samtools_stats false \
+        --samtools_coverage false \
+        --samtools_depth false \
+        --nextclade false \
+        --pangolin false \
+        --freyja false \
+        --vadr false \
+        -resume \
+        -with-tower
+    done
+
+    mpx_primers=("mpx_primalseq" "mpx_idt")
+    for primer in ${mpx_primers[@]}
+    do
+      nextflow run ~/sandbox/Cecret \
+        -profile singularity \
+        --reads /home/eriny/sandbox/test_files/cecret/mpx_idt \
+        --outdir primer_${primer}_${trimmer} \
+        --trimmer $trimmer \
+        --cleaner 'fastp' \
+        --primer_set $primer \
+        --bcftools_variants false \
+        --fastqc false \
+        --ivar_variants false \
+        --samtools_stats false \
+        --samtools_coverage false \
+        --samtools_depth false \
+        --nextclade false \
+        --pangolin false \
+        --freyja false \
+        --vadr false \
+        -with-tower \
+        -resume
+    done
+  done
+
 else
   # CDC's test data with relatedness
   nextflow run ~/sandbox/Cecret \
diff --git a/bin/params.sh b/bin/params.sh
new file mode 100755
index 00000000..e20c674a
--- /dev/null
+++ b/bin/params.sh
@@ -0,0 +1,82 @@
+#!/bin/bash
+
+##### ##### ##### ##### ##### ##### ##### ##### #####
+# It's like nf-core's version, but jankier      #####
+##### ##### ##### ##### ##### ##### ##### ##### #####
+
+# this 
+# 1. finds all the params
+# 2. checks that they are in nextflow_schema.json
+# 3. checks that their default value is in nextflow_schema.json
+# 4. checks that every param and its default value is in the config file
+# 5. checks that every process with its default values are in the config file
+
+##### ##### ##### ##### ##### ##### ##### ##### #####
+# finding all the params                        #####
+##### ##### ##### ##### ##### ##### ##### ##### #####
+
+params=$(grep param main.nf | awk '{ ( $1=$1 ) ; print $0 }' | grep ^param | awk '{print $1}' | sort | uniq | cut -f 2 -d '.')
+
+for param in ${params[@]}
+do
+    echo "evaluating params.$param"
+
+    # default value
+    default="$(grep -w params.$param main.nf | grep "=" | head -n 1 | sed 's/.*=//g' | awk '{ ( $1=$1 ) ; print $0 }' ) "
+    echo -e "default:\t$default"
+
+    # 2. checks that they are in nextflow_schema.json
+    schema_check=$(grep "\"$param\":" nextflow_schema.json | head -n 1)
+    if [ -n "$schema_check" ]
+    then
+        # 3. checks that their default value is in nextflow_schema.json
+        schema_default="$(grep "\"$param\":" -A 10 nextflow_schema.json | grep "}" -B 10 -m 1 | grep "default" | head -n 1 | sed 's/.*://g' | awk '{ ( $1=$1 ) ; print $0 }'  )"
+        echo -e "schema:\t\t$schema_default"
+       
+    else
+        echo "$param was not included in nextflow_schema.json file!!!"
+    fi
+
+    config_check=$(grep "params.$param =" configs/cecret_config_template.config | head -n 1)
+    if [ -n "$config_check" ]
+    then
+        # 4. checks that every param and its default value is in the config file
+        config_default="$(grep -w params.$param configs/cecret_config_template.config | grep -v "#" | head -n 1 | sed 's/.*=//g' | awk '{ ( $1=$1 ) ; print $0 }' )"
+        echo -e "config:\t\t$config_default"
+       
+    else
+        echo "$param was not included in configs/cecret_config_template.config file!!!"
+    fi
+
+    echo ""
+
+done
+
+echo "##### ##### ##### ##### #####"
+echo "# Now for the processes #####"
+echo "##### ##### ##### ##### #####"
+
+
+processes=$(grep ^process -h modules/*nf | awk '{print $2}' | sort | uniq )
+echo ${processes[@]}
+
+for process in ${processes[@]}
+do
+    #echo "getting information for $process"
+    #grep "process $process {" -h modules/*nf -A 200 | grep -e "when:" -e "input:" -B 200 -m 1 | grep -v "#UPHLICA" | grep -v "when:" | grep -v "input:" | grep -v "tag"
+
+    echo -e "//\twithName:$process{"
+    while read line
+    do
+        key=$(echo $line | awk '{print $1}' | grep -v process )
+        if [ -n "$key" ]
+        then
+            value=$(echo $line | sed "s|$key||g" | awk '{ ( $1=$1 ) ; print $0 }' | sed 's/\"${params.outdir}\"/cecret/g')
+            echo -e "//\t\t$key = \"$value\""
+        fi
+    done < <(grep "process $process {" -h modules/*nf -A 200 | grep -e "when:" -e "input:" -B 200 -m 1 | grep -v "#UPHLICA" | grep -v "when:" | grep -v "input:" | grep -v "tag")
+    echo -e "//\t}"
+
+    #echo ""
+    #grep "//  withName:$process{" -A 20 configs/cecret_config_template.config | grep -m 1 "}" -B 20
+done
\ No newline at end of file
diff --git a/configs/cecret_config_template.config b/configs/cecret_config_template.config
index d7c45b31..845cf80b 100644
--- a/configs/cecret_config_template.config
+++ b/configs/cecret_config_template.config
@@ -1,3 +1,16 @@
+//# Instructions --------------------------------------------
+//# We think it's great that you want to adjust some paramaters.
+//# This is very useful when running this on the cloud.
+//# This is especially useful for the following processes:
+//#     - params.kraken2_db to specify where the kraken2 database is on your system
+//#     - params.artic_options to specify what flow cell was used to generate nanopore reads
+//#     - the organism-specific files for non-COVID/MPX isolates
+//# Right now, most everything is commented out with '//'.
+//# To adjust a parameter, remove the '//' from in front of a param and replace the value
+//# with the one that suits your needs.
+//# Don't hesitate to ask for assistance at https://github.com/UPHL-BioNGS/Cecret/issues
+//# if something doesn't work (also, please include a copy of your config file).
+
 //# Docker Params -------------------------------------------
 //# see https://www.nextflow.io/docs/latest/config.html#scope-docker for a complete list
 //docker.enabled = true
@@ -50,7 +63,11 @@
 //params.reads = 'reads'
 //params.single_reads = 'single_reads'
 //params.fastas = 'fastas'
+//params.multifastas = 'multifastas'
+//params.nanopore = 'nanopore'
+//params.sample_sheet = "sample_sheet.csv"
 //params.outdir = 'cecret'
+//params.sra_accessions = []
 
 //# Basic CPU usage grouping
 //params.maxcpus = 8
@@ -59,11 +76,14 @@
 //# Specifying the 'sarscov2', 'mpx', or 'other'
 //params.species = 'sarscov2'
 
+//# using the included primer sets
+//params.primer_set = "ncov_V4"
+
 //# Reference files for SARS-CoV-2 (part of the github repository)
-//params.reference_genome = "Cecret/configs/MN908947.3.fasta"
-//params.gff_file = "Cecret/configs/MN908947.3.gff"
-//params.primer_bed = "Cecret/configs/artic_V3_nCoV-2019.bed"
-//params.amplicon_bed = "Cecret/configs/nCoV-2019.insert.bed"
+//params.reference_genome = "< path/to/file >"
+//params.gff = "< path/to/file >"
+//params.primer_bed = "< path/to/file >"
+//params.amplicon_bed = "< path/to/file >"
 
 //# Tool toggles
 //# trimmer options are 'ivar' and 'samtools' or 'none' for no primer trimming
@@ -127,7 +147,7 @@
 //params.minimum_depth = 100
 //# params.mpileup_depth is shared with ivar_consensus and bcftools_variants
 //params.mpileup_depth = 8000
-//params.ivar_variants_options = '-q 20 -t 0.6 '
+//params.ivar_variants_options = '-q 20 -t 0.6'
 
 //# For process ivar_consensus
 //# params.minimum_depth is shared with ivar_variants, summary, and samtools_depth
@@ -139,8 +159,16 @@
 //# For process fasta_prep
 //# No editable parameters
 
+//# For process aci
+//params.aci = true
+
+//# For processes artic and artic_read_filtering
+//params.artic_options = "--normalise 200 --skip-nanopolish --medaka --medaka-model r941_min_high_g360"
+//params.artic_read_filtering_options = "--min-length 400 --max-length 700"
+
 //# For process bcftools_variants
 //params.bcftools_variants = true
+//params.bcftools_variants_options = ""
 //# params.mpileup_depth is shared with ivar_variants and ivar_consensus
 //params.mpileup_depth = 8000
 
@@ -164,13 +192,8 @@
 
 //# For process kraken2
 //params.kraken2_options = ''
-//params.kraken2 = true
-//params.kraken2_db = ''
-//params.kraken2_organism = "Severe acute respiratory syndrome-related coronavirus"
-
-//# For process bedtools_multicov
-//params.bedtools_multicov = true
-//params.bedtools_options = '-f .1'
+//params.kraken2 = false
+//params.kraken2_db = false
 
 //# For process samtools_ampliconstats and samtools_plot_ampliconstats
 //params.samtools_ampliconstats_options = ''
@@ -183,19 +206,20 @@
 //params.pangolin = true
 
 //# For process freyja and freyja_aggregate
-//params.freya = true
+//params.freyja = true
 //params.freyja_aggregate = true
-//params.freyja_variants_options=''
-//params.freyja_demix_options=''
-//params.freyja_boot_options='--nb 1000'
-//params.freyja_aggregate_options=''
-//params.freyja_plot_options=''
-//params.freyja_plot_filetype='png'
+//params.freyja_variants_options = ''
+//params.freyja_demix_options = '--depthcutoff 100'
+//params.freyja_boot_options = '--nb 1000 --depthcutoff 100'
+//params.freyja_aggregate_options = ''
+//params.freyja_plot_options = '--mincov 100'
+//params.freyja_plot_filetype = 'png'
 
 //# For process nextclade
 //params.nextclade_dataset = 'sars-cov-2'
 //params.nextclade_options = ''
 //params.nextclade = true
+//params.download_nextclade_dataset = false
 
 //# For process vadr
 //params.vadr_options = '--split --glsearch -s -r --nomisc --lowsim5seq 6 --lowsim3seq 6 --alt_fail lowscore,insertnn,deletinn'
@@ -232,120 +256,212 @@
 //params.multiqc = true
 //params.multiqc_options = ''
 
-//# ------------------------------------------------------------------------
-//# Examples of how to change containers or process directive values -------
-//# This is likely not current and should not be used as-is ----------------
-//# You've been warned <3 --------------------------------------------------
-
-//# Docker Images -------------------------------------------
-//# static containers (may become out of date)
-//bcftools_container      = 'staphb/bcftools:1.16'
-//bedtools_container      = 'staphb/bedtools:2.30.0'
-//bwa_container           = 'staphb/bwa:0.7.17'
-//fastp_container         = 'staphb/fastp:0.23.2'
-//fastqc_container        = 'staphb/fastqc:0.11.9'
-//freyja_container        = 'staphb/freyja:1.3.11'
-//iqtree2_container       = 'staphb/iqtree2:2.1.2'
-//ivar_container          = 'staphb/ivar:1.3.1'
-//kraken2_container       = 'staphb/kraken2:2.1.2-no-db'
-//mafft_container         = 'staphb/mafft:7.475'
-//minimap2_container      = 'staphb/minimap2:2.24'
-//multiqc_container       = 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0'
-//pandas_container        = 'quay.io/biocontainers/pandas:1.1.5'
-//samtools_container      = 'staphb/samtools:1.16'
-//seqyclean_container     = 'staphb/seqyclean:1.10.09'
-//snp_dists_container     = 'staphb/snp-dists:0.8.2'
-//vadr_container          = 'staphb/vadr:1.5'
-
-//# latest tags (more likely to break workflow, but they update "too frequently")
-//nextalign_container     = 'nextstrain/nextalign:latest'
-//nextclade_container     = 'nextstrain/nextclade:latest'
-//pangolin_container      = 'staphb/pangolin:latest'
-
-
-//# Changing the directives for processes
-//# The processes can be found in Grandeur/modules and their names are
-//bcftools_variants
-//bedtools_multicov
-//bwa
-//fasta_prep
-//summary
-//combine_results
-//download
-//fastp
-//fastqc
-//freyja
-//freyja_aggregate
-//iqtree2
-//ivar_consensus
-//ivar_variants
-//ivar_trim
-//kraken2
-//mafft
-//minimap2
-//multiqc_combine
-//nextalign
-//nextclade
-//pangolin
-//samtools_stats
-//samtools_coverage
-//samtools_flagstat
-//samtools_depth
-//samtools_ampliconstats
-//samtools_plot_ampliconstats
-//samtools_sort
-//samtools_filter
-//samtools_ampliconclip
-//samtools_markdup
-//seqyclean
-//snpdists
-//vadr
-
 //# Adjusting the directives for a process
-//# seehttps://www.nextflow.io/docs/latest/config.html#scope-process
+//# see https://www.nextflow.io/docs/latest/config.html#scope-process
+//# WARNING : THIS WAS PUT TOGETHER IN A HURRY AND LIKELY HAS TYPOS!!!
 //process {
-//  publishDir = [ path: params.outdir, mode: 'copy' ]
-//
-//  errorStrategy = 'retry'
-//  maxRetries = 1
 //
-//  withLabel: maxcpus {
+//  withLabel:maxcpus{
 //    cpus = params.maxcpus
 //  }
-//  withLabel: medcpus {
+//  withLabel:medcpus{
 //    cpus = params.medcpus
 //  }
 //
-//  withName:download {
-//    container = pandas_container
-//  }
-//
-//  withName:fastqc{
-//    container = fastqc_container
-//  }
-//
-//  withName:bwa{
-//    container = bwa_container
-//    publishDir = [ path: "${params.outdir}", mode: 'copy', pattern: 'logs/*/*log' ]
-//  }
-//
-//  withName:minimap2{
-//    container = minimap2_container
-//    publishDir = [ path: "${params.outdir}", mode: 'copy', pattern: 'logs/*/*log' ]
-//  }
-//
-//  withName:'ivar_.*'{
-//    container = ivar_container
-//  }
-//
-//  withName:vadr{
-//    container = vadr_container
-//    errorStrategy = 'ignore'
-//  }
-//
-//  withName:mafft{
-//    container = mafft_container
-//    errorStrategy = 'retry'
-//    maxRetries = 2
-//  }
+//	withName:aci{
+//		label = "process_high"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "quay.io/erinyoung/aci:0.1.20230815"
+//	}
+//	withName:artic{
+//		label = "process_high"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "quay.io/uphl/artic:1.2.4-1.9.4-1"
+//	}
+//	withName:artic_read_filtering{
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "quay.io/uphl/artic:1.2.4-1.9.4-1"
+//		label = "process_single"
+//	}
+//	withName:bcftools_variants{
+//		publishDir = "cecret, mode: 'copy'"
+//		errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
+//		container = "staphb/bcftools:1.18"
+//		label = "process_single"
+//	}
+//	withName:bwa{
+//		label = "process_high"
+//		publishDir = "path: cecret, mode: 'copy', pattern: 'logs/*/*log'"
+//		container = "staphb/bwa:0.7.17"
+//	}
+//	withName:download{
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "quay.io/uphl/seaborn:0.12.2"
+//		label = "process_single"
+//	}
+//	withName:fasta_prep{
+//		container = "quay.io/uphl/seaborn:0.12.2"
+//		label = "process_single"
+//	}
+//	withName:fastp{
+//		label = "process_single"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/fastp:0.23.4"
+//	}
+//	withName:fastqc{
+//		label = "process_single"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/fastqc:0.12.1"
+//	}
+//	withName:freyja{
+//		label = "process_medium"
+//		errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "quay.io/uphl/freyja:1.4.7-2023-09-26"
+//	}
+//	withName:freyja_aggregate{
+//		label = "process_single"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "quay.io/uphl/freyja:1.4.7-2023-09-26"
+//	}
+//	withName:iqtree2{
+//		label = "process_high"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/iqtree2:2.2.2.6"
+//	}
+//	withName:ivar_consensus{
+//		label = "process_medium"
+//		memory = "{ 2.GB * task.attempt }"
+//		errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
+//		publishDir = "params.outdir, mode: 'copy'"
+//		container = "staphb/ivar:1.4.2"
+//	}
+//	withName:ivar_trim{
+//		label = "process_medium"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/ivar:1.4.2"
+//	}
+//	withName:ivar_variants{
+//		label = "process_medium"
+//		memory = "{ 2.GB * task.attempt }"
+//		errorStrategy = "{ task.attempt < 3 ? 'retry' : 'ignore'}"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/ivar:1.4.2"
+//	}
+//	withName:kraken2{
+//		label = "process_high"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/kraken2:2.1.3"
+//	}
+//	withName:mafft{
+//		label = "process_high"
+//		errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/mafft:7.505"
+//	}
+//	withName:minimap2{
+//		label = "process_high"
+//		publishDir = "[ path: cecret, mode: 'copy', pattern: 'logs/*/*log' ]"
+//		container = "staphb/minimap2:2.25"
+//	}
+//	withName:multiqc_combine{
+//		label = "process_single"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "quay.io/bios/multiqc:1.14--pyhdfd78af_0"
+//	}
+//	withName:nextalign{
+//		label = "process_high"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "nextstrain/nextalign:2.14.0"
+//	}
+//	withName:nextclade{
+//		label = "process_medium"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "nextstrain/nextclade:2.14.0"
+//	}
+//	withName:nextclade_dataset{
+//		label = "process_medium"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "nextstrain/nextclade:2.14.0"
+//	}
+//	withName:pangolin{
+//		label = "process_medium"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/pangolin:4.3.1-pdata-1.22"
+//	}
+//	withName:samtools_ampliconclip{
+//		label = "process_single"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/samtools:1.17"
+//	}
+//	withName:samtools_ampliconstats{
+//		label = "process_single"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/samtools:1.17"
+//	}
+//	withName:samtools_coverage{
+//		label = "process_single"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/samtools:1.17"
+//	}
+//	withName:samtools_depth{
+//		label = "process_single"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/samtools:1.17"
+//	}
+//	withName:samtools_filter{
+//		label = "process_single"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/samtools:1.17"
+//	}
+//	withName:samtools_flagstat{
+//		label = "process_single"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/samtools:1.17"
+//	}
+//	withName:samtools_markdup{
+//		label = "process_single"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/samtools:1.17"
+//	}
+//	withName:samtools_plot_ampliconstats{
+//		label = "process_single"
+//		errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/samtools:1.17"
+//	}
+//	withName:samtools_sort{
+//		label = "process_high"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/samtools:1.17"
+//	}
+//	withName:samtools_stats{
+//		label = "process_single"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/samtools:1.17"
+//	}
+//	withName:seqyclean{
+//		label = "process_single"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/seqyclean:1.10.09"
+//	}
+//	withName:snpdists{
+//		label = "process_single"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/snp-dists:0.8.2"
+//	}
+//	withName:summary{
+//		label = "process_single"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "quay.io/uphl/seaborn:0.12.2"
+//	}
+//	withName:unzip{
+//		label = "process_single"
+//		container = "quay.io/uphl/seaborn:0.12.2"
+//	}
+//	withName:vadr{
+//		label = "process_medium"
+//		publishDir = "cecret, mode: 'copy'"
+//		container = "staphb/vadr:1.5.1"
+//	}
 //}
diff --git a/main.nf b/main.nf
index 126fa9fa..7d87c733 100644
--- a/main.nf
+++ b/main.nf
@@ -10,7 +10,7 @@ println(' \\____|_____\\____|_| \\_\\_____| |_|')
 
 println('Version: ' + workflow.manifest.version)
 println('')
-println('Currently using the Cecret workflow for use with amplicon Illumina library prep on MiSeq with a corresponding reference genome.\n')
+println('Currently using the Cecret workflow for use with corresponding reference genome.\n')
 println('Author: Erin Young')
 println('email: eriny@utah.gov')
 println('')
@@ -178,10 +178,10 @@ params.vadr_mdir                            = '/opt/vadr/vadr-models'
 params.nextclade_options                    = ''
 params.nextalign_options                    = '--include-reference'
 params.freyja_variants_options              = ''
-params.freyja_demix_options                 = ''
-params.freyja_boot_options                  = '--nb 1000'
+params.freyja_demix_options                 = "--depthcutoff ${params.minimum_depth}"
+params.freyja_boot_options                  = "--nb 1000 --depthcutoff ${params.minimum_depth}"
 params.freyja_aggregate_options             = ''
-params.freyja_plot_options                  = ''
+params.freyja_plot_options                  = "--mincov ${params.minimum_depth}"
 params.freyja_plot_filetype                 = 'png'
 
 //# Specifying some species-specific params
diff --git a/modules/aci.nf b/modules/aci.nf
index 5b1ebdc7..67721833 100644
--- a/modules/aci.nf
+++ b/modules/aci.nf
@@ -3,9 +3,9 @@ process aci {
     label      "process_high"
     publishDir "${params.outdir}", mode: 'copy'
     container  'quay.io/erinyoung/aci:0.1.20230815'
+    errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   
     //#UPHLICA maxForks      10
-    //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
     //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
     //#UPHLICA memory 60.GB
     //#UPHLICA cpus 14
diff --git a/modules/artic.nf b/modules/artic.nf
index dd47eb94..1734eb8e 100644
--- a/modules/artic.nf
+++ b/modules/artic.nf
@@ -15,8 +15,8 @@ process artic {
     tuple val(sample), file(fastq), file(reference), file(bed)
 
     output:
-    tuple val(sample), file("artic/${sample}.primertrim.sorted.bam"), file("artic/${sample}.primertrim.sorted.bam.bai"), emit: bam
-    path "consensus/${sample}.consensus.fa", emit: consensus
+    tuple val(sample), file("artic/${sample}.primertrim.sorted.bam"), file("artic/${sample}.primertrim.sorted.bam.bai"), emit: bam, optional: true
+    path "consensus/${sample}.consensus.fa", emit: consensus, optional: true
     tuple val("artic"), env(artic_version), emit: artic_version
     path "artic/${sample}*"
     path "logs/${task.process}/${sample}.${workflow.sessionId}.log"
diff --git a/modules/bwa.nf b/modules/bwa.nf
index cc8e8b20..0bf68ebc 100644
--- a/modules/bwa.nf
+++ b/modules/bwa.nf
@@ -1,8 +1,8 @@
 process bwa {
-  tag        "${sample}"
-  label      "process_high"
-  publishDir = [ path: "${params.outdir}", mode: 'copy', pattern: 'logs/*/*log' ]
-  container  'staphb/bwa:0.7.17'
+  tag         "${sample}"
+  label       "process_high"
+  publishDir  path: "${params.outdir}", mode: 'copy', pattern: 'logs/*/*log'
+  container   'staphb/bwa:0.7.17'
   
   //#UPHLICA maxForks 10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
diff --git a/modules/freyja.nf b/modules/freyja.nf
index 796cc5d7..1f165733 100644
--- a/modules/freyja.nf
+++ b/modules/freyja.nf
@@ -3,7 +3,7 @@ process freyja {
   label         "process_medium"
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   publishDir    "${params.outdir}", mode: 'copy'
-  container     'quay.io/uphl/freyja:1.4.7-20230915'
+  container     'quay.io/uphl/freyja:1.4.7-2023-09-26'
 
   //#UPHLICA maxForks 10
   //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
@@ -44,7 +44,7 @@ process freyja {
       --output freyja/!{sample}_demix.tsv \
       | tee -a $log
 
-    freyja boot \
+    freyja boot !{params.freyja_boot_options} \
       freyja/!{sample}_variants.tsv \
       freyja/!{sample}_depths.tsv \
       --nt !{task.cpus} \
@@ -57,7 +57,7 @@ process freyja_aggregate {
   tag        "Aggregating results from freyja"
   label      "process_single"
   publishDir "${params.outdir}", mode: 'copy'
-  container  'quay.io/uphl/freyja:1.4.7-20230915'
+  container  'quay.io/uphl/freyja:1.4.7-2023-09-26'
 
   //#UPHLICA maxForks 10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
diff --git a/modules/minimap2.nf b/modules/minimap2.nf
index 4842401f..5319c3c9 100644
--- a/modules/minimap2.nf
+++ b/modules/minimap2.nf
@@ -1,8 +1,8 @@
 process minimap2 {
-  tag        "${sample}"
-  label      "process_high"
-  publishDir = [ path: "${params.outdir}", mode: 'copy', pattern: 'logs/*/*log' ]
-  container  'staphb/minimap2:2.25'
+  tag         "${sample}"
+  label       "process_high"
+  publishDir  path: "${params.outdir}", mode: 'copy', pattern: 'logs/*/*log'
+  container   'staphb/minimap2:2.25'
 
   //#UPHLICA maxForks 10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
diff --git a/nextflow.config b/nextflow.config
index aa5c2f96..a4f9262a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -5,7 +5,7 @@ manifest {
   name              = 'Cecret'
   author            = 'Erin Young'
   homePage          = 'https://github.com/UPHL-BioNGS/Cecret'
-  version           = 'v3.8.20230915'
+  version           = 'v3.8.20230926'
   defaultBranch     = 'master'
   recurseSubmodules = false
   description       = 'Reference-based consensus creation'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index fb1c60bb..b734f3f5 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -30,7 +30,7 @@
             "type": "string",
             "description": "Options for process",
             "hidden": true,
-            "default": "--normalise 200 --skip-nanopolish"
+            "default": "--normalise 200 --skip-nanopolish --medaka --medaka-model r941_min_high_g360"
         },
         "artic_read_filtering_options": {
             "type": "string",
@@ -62,13 +62,14 @@
         "config_file": {
             "type": "boolean",
             "hidden": true,
+            "default": false,
             "description" : "Specifies if a config file is copied for the end user. Ends script."
         },
         "download_nextclade_dataset": {
             "type": "boolean",
             "hidden": false,
             "description" : "Specifies if nextclade should download its dataset. Set to false to use included dataset.",
-            "default" : true
+            "default" : false
         },
         "fastas": { 
             "type": "string",
@@ -121,17 +122,19 @@
         "freyja_boot_options": { 
             "type": "string",
             "hidden": true,
-            "default": "--nb 1000",
+            "default": "--nb 1000 --depthcutoff 100",
             "description": "Options for process"
         },
         "freyja_demix_options": { 
             "type": "string",
             "hidden": true,
+            "default": "--depthcutoff 100",
             "description": "Options for process"
         },
         "freyja_plot_filetype": { 
             "type": "string",
             "hidden": true,
+            "default": "png",
             "description": "Specifies filetype for freyja plot",
             "enum": [
                 ".pdf", 
@@ -141,7 +144,7 @@
         "freyja_plot_options": { 
             "type": "string",
             "hidden": true,
-            "default": "png",
+            "default": "--mincov 100",
             "description": "Options for process"
         },
         "freyja_variants_options": { 
@@ -169,6 +172,7 @@
         "iqtree2_outgroup": { 
             "type": "string",
             "hidden": true,
+            "default": "MN908947",
             "description": "outgroup for multiple sequence alignment"
         },
         "ivar_consensus_options": { 
@@ -200,7 +204,8 @@
             "description": "Specifies if process should be used"
         },
         "kraken2_db": { 
-            "type": "string", 
+            "type": "string",
+            "default": "false",
             "description": "directory to kraken2 database"
         },
         "kraken2_options": { 
@@ -295,6 +300,7 @@
         "nextclade_dataset": { 
             "type": "string",
             "hidden": true,
+            "default": "sars-cov-2",
             "description": "Specifies nextclade dataset"
         },
         "nextclade_options": { 
@@ -303,7 +309,8 @@
             "description": "Options for process"
         },
         "outdir": { 
-            "type": "string", 
+            "type": "string",
+            "default": "cecret",
             "description": "Specifies where results are saved"
         },
         "pangolin": { 
@@ -408,6 +415,12 @@
             "hidden": true,
             "description": "Options for process"
         },
+        "samtools_flagstat": {
+            "type": "boolean",
+            "hidden": true,
+            "default": true,
+            "description": "Specifies if process should be used"
+        },
         "samtools_flagstat_options": { 
             "type": "string",
             "hidden": true,
@@ -439,7 +452,6 @@
         "samtools_stats_options": { 
             "type": "string",
             "hidden": true,
-            "default": true,
             "description": "Options for process"
         },
         "seqyclean_contaminant_file": { 
@@ -500,6 +512,7 @@
         "vadr": { 
             "type": "boolean",
             "hidden": true,
+            "default": true,
             "description": "Specifies if process should be used"
         },
         "vadr_mdir": { 
@@ -511,15 +524,18 @@
         "vadr_options": { 
             "type": "string",
             "hidden": true,
+            "default": "--split --glsearch -s -r --nomisc --lowsim5seq 6 --lowsim3seq 6 --alt_fail lowscore,insertnn,deletinn",
             "description": "Options for process"
         },
         "vadr_reference": { 
             "type": "string",
             "hidden": true,
+            "default": "sarscov2",
             "description": "Specifies reference for vadr in container"
         },
         "vadr_trim_options": { 
             "type": "string",
+            "default": "--minlen 50 --maxlen 30000",
             "hidden": true,
             "description": "Options for process"
         }
diff --git a/schema/midnight_ont_V2_SARS-CoV-2.insert.bed b/schema/midnight_ont_V2_SARS-CoV-2.insert.bed
index 2a32c97d..4fa3b0e4 100644
--- a/schema/midnight_ont_V2_SARS-CoV-2.insert.bed
+++ b/schema/midnight_ont_V2_SARS-CoV-2.insert.bed
@@ -27,4 +27,3 @@ MN908947.3	25712	26835	nCoV-2019_26_INSERT	26	+
 MN908947.3	26766	27872	nCoV-2019_27_INSERT	27	+
 MN908947.3	27808	28985	nCoV-2019_28_INSERT	28	+
 MN908947.3	28699	29768	nCoV-2019_29_INSERT	29	+
-				1	+
diff --git a/schema/midnight_ont_V2_SARS-CoV-2.primer.bed~ b/schema/midnight_ont_V2_SARS-CoV-2.primer.bed~
deleted file mode 100644
index 91846059..00000000
--- a/schema/midnight_ont_V2_SARS-CoV-2.primer.bed~
+++ /dev/null
@@ -1,59 +0,0 @@
-MN908947.3	30	54	nCoV-2019_1_LEFT	1	
-MN908947.3	1183	1205	nCoV-2019_1_RIGHT	1	
-MN908947.3	1100	1128	nCoV-2019_2_LEFT	2	
-MN908947.3	2244	2266	nCoV-2019_2_RIGHT	2	
-MN908947.3	2153	2179	nCoV-2019_3_LEFT	1	
-MN908947.3	3235	3257	nCoV-2019_3_RIGHT	1	
-MN908947.3	3144	3166	nCoV-2019_4_LEFT	2	
-MN908947.3	4240	4262	nCoV-2019_4_RIGHT	2	
-MN908947.3	4167	4189	nCoV-2019_5_LEFT	1	
-MN908947.3	5337	5359	nCoV-2019_5_RIGHT	1	
-MN908947.3	5257	5286	nCoV-2019_6_LEFT	2	
-MN908947.3	6358	6380	nCoV-2019_6_RIGHT	2	
-MN908947.3	6283	6307	nCoV-2019_7_LEFT	1	
-MN908947.3	7379	7401	nCoV-2019_7_RIGHT	1	
-MN908947.3	7298	7328	nCoV-2019_8_LEFT	2	
-MN908947.3	8363	8385	nCoV-2019_8_RIGHT	2	
-MN908947.3	8253	8282	nCoV-2019_9_LEFT	1	
-MN908947.3	9378	9400	nCoV-2019_9_RIGHT	1	
-MN908947.3	9303	9327	nCoV-2019_10_LEFT	2	
-MN908947.3	10429	10451	nCoV-2019_10_RIGHT	2	
-MN908947.3	10343	10370	nCoV-2019_11_LEFT	1	
-MN908947.3	11447	11469	nCoV-2019_11_RIGHT	1	
-MN908947.3	11372	11394	nCoV-2019_12_LEFT	2	
-MN908947.3	12538	12560	nCoV-2019_12_RIGHT	2	
-MN908947.3	12450	12473	nCoV-2019_13_LEFT	1	
-MN908947.3	13599	13621	nCoV-2019_13_RIGHT	1	
-MN908947.3	13509	13532	nCoV-2019_14_LEFT	2	
-MN908947.3	14619	14641	nCoV-2019_14_RIGHT	2	
-MN908947.3	14540	14568	nCoV-2019_15_LEFT	1	
-MN908947.3	15713	15735	nCoV-2019_15_RIGHT	1	
-MN908947.3	15608	15634	nCoV-2019_16_LEFT	2	
-MN908947.3	16698	16720	nCoV-2019_16_RIGHT	2	
-MN908947.3	16624	16647	nCoV-2019_17_LEFT	1	
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