diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 3a049c4..6314c1a 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -19,16 +19,16 @@ jobs:
           java-version: '17'
           distribution: 'adopt'
 
-      - name: Set up Apptainer 1.3.0
+      - name: Set up Apptainer 1.3.6
         uses: eWaterCycle/setup-apptainer@v2
         with:
-          apptainer-version: 1.3.0
+          apptainer-version: 1.3.6
 
 
       - name: Setup Nextflow 24.10.1
         uses: nf-core/setup-nextflow@v1
         with:
-          version: "24.10.1"
+          version: "24.10.3"
 
       - name: Install nf-test
         run: |
diff --git a/main.nf b/main.nf
index eb5a500..1e2fa9d 100644
--- a/main.nf
+++ b/main.nf
@@ -9,30 +9,30 @@ include {READSTOCONTIGS} from './modules/runReadsToContig/runReadsToContig.nf'
 
 workflow {
 
-    //input specification
-
-    pairedFiles = channel.fromPath(params.pairedFiles, checkIfExists:true)
-    unpairedFiles = channel.fromPath(params.unpairedFiles, checkIfExists:true)
+    //input specification    
+    fastqFiles = channel.fromPath(params.shared.inputFastq, checkIfExists:true)
     contigs = channel.empty()
     if(params.r2c.useAssembledContigs) {
-        contigs = channel.fromPath(params.inputContigs, checkIfExists:true)
+        contigs = channel.fromPath(params.shared.inputContigs, checkIfExists:true)
     }
 
+
     if(params.modules.sra2fastq) {
         SRA2FASTQ(params.sra2fastq.plus(params.shared))
-        pairedFiles = pairedFiles.concat(SRA2FASTQ.out.paired).flatten()
-        unpairedFiles = unpairedFiles.concat(SRA2FASTQ.out.unpaired).flatten()
+        fastqFiles = fastqFiles.concat(SRA2FASTQ.out.fastq).flatten()
     }
     
-    COUNTFASTQ(pairedFiles.collect(), unpairedFiles.collect())
+    COUNTFASTQ(params.shared, fastqFiles.collect())
 
     avgLen = COUNTFASTQ.out.avgReadLen
-    paired = COUNTFASTQ.out.paired.ifEmpty(params.pairedFiles)
-    unpaired = COUNTFASTQ.out.unpaired.ifEmpty(params.unpairedFiles)
+    fastqFiles = COUNTFASTQ.out.fastqFiles
 
 
+    paired = channel.empty()
+    unpaired = channel.empty()
     if(params.modules.faqcs) {
-        FAQCS(params.faqcs.plus(params.shared),paired,unpaired,avgLen)
+        FAQCS(params.faqcs.plus(params.shared), fastqFiles,avgLen)
+
         paired = FAQCS.out.paired.ifEmpty(params.pairedFiles)
         unpaired = FAQCS.out.unpaired.ifEmpty(params.unpairedFiles)
     }
diff --git a/modules/countFastq/countFastq.nf b/modules/countFastq/countFastq.nf
index 3eb4f80..2c177d1 100644
--- a/modules/countFastq/countFastq.nf
+++ b/modules/countFastq/countFastq.nf
@@ -3,37 +3,26 @@ process countFastq {
     label "countFastq"
 
     input:
-    path paired
-    path unpaired
+    val settings
+    path fastq
 
     output:
     path "fastqCount.txt", emit: counts
-    path "all.{1,2}.fastq", emit: allPaired, optional:true
-    path "all.se.fastq", emit: allUnpaired, optional:true
+    path "all.*.fastq", emit: allFiles
 
     script:
 
-    if(paired.size() > 1 && paired[0] =~ /NO_FILE/) {
-        paired = paired.tail().join(" ")
+    file_list = ""
+    if(settings["pairedFile"]) {
+        file_list = "-p $fastq"
     }
     else {
-        paired = paired.join(" ")
+        file_list = "-u $fastq"
     }
-    if(unpaired.size() > 1 && unpaired[0] =~ /NO_FILE/) {
-        unpaired = unpaired.tail().join(" ")
-    }
-    else {
-        unpaired = unpaired.join(" ")
-    }
-    
-
-    paired_list = paired.startsWith("NO_FILE") ? "" : "-p ${paired}"
-    unpaired_list = unpaired.startsWith("NO_FILE2") ? "" : "-u ${unpaired}"
 
     """
     getAvgLen.pl\
-    $paired_list\
-    $unpaired_list\
+    $file_list\
     -d .
     """
 }
@@ -70,19 +59,16 @@ process avgLen {
 //calculates average read length and concatenates input files
 workflow COUNTFASTQ {
     take:
-    pairedFiles
-    unpairedFiles
+    settings
+    inputFastq
 
     main:
 
-    countFastq(pairedFiles, unpairedFiles)
+    countFastq(settings, inputFastq)
     avgReadLen = avgLen(countFastq.out.counts)
-    paired = countFastq.out.allPaired
-    unpaired = countFastq.out.allUnpaired
-
+    fastqFiles = countFastq.out.allFiles
 
     emit:
     avgReadLen
-    paired
-    unpaired
+    fastqFiles
 }
\ No newline at end of file
diff --git a/modules/hostRemoval/hostRemoval.nf b/modules/hostRemoval/hostRemoval.nf
index 3b3083f..0b1986f 100644
--- a/modules/hostRemoval/hostRemoval.nf
+++ b/modules/hostRemoval/hostRemoval.nf
@@ -35,10 +35,17 @@ process hostRemoval {
     def prefix = "-prefix ${ref.name.take(ref.name.lastIndexOf('.'))}.clean "
     def similarity = settings["similarity"] != null ? "-similarity ${settings["similarity"]} " : ""
     def minScore = settings["bwaMemOptions"] != null ? "${settings["bwaMemOptions"]} " : "-T 50 "
-    def ontFlag = settings["fastqSource"].equalsIgnoreCase("nanopore") ? "-x ont2d " : ""
-    ontFlag = settings["fastqSource"].equalsIgnoreCase("pacbio") ? "-x pacbio " : ontFlag
+    ontFlag = ""
+    if(settings["fastqSource"] != null) {
+        if(settings["fastqSource"].equalsIgnoreCase("nanopore")) {
+            ontFlag = "-x ont2d "
+        }
+        else if(settings["fastqSource"].equalsIgnoreCase("pacbio")) {
+            ontFlag = "-x pacbio "
+        }
+    }
     minScore = ontFlag != "" ? "-T ${settings["minLen"]} " : minScore
-    def bwaMemOptions = "-bwaMemOptions \"${ontFlag} ${minScore}\" "
+    bwaMemOptions = "-bwaMemOptions \"${ontFlag} ${minScore}\" "
     def cpu = settings["cpus"] != null ? "-cpu ${settings["cpus"]} " : ""
     
     """
diff --git a/modules/runFaQCs/runFaQCs.nf b/modules/runFaQCs/runFaQCs.nf
index e0e6fb9..4ea188c 100644
--- a/modules/runFaQCs/runFaQCs.nf
+++ b/modules/runFaQCs/runFaQCs.nf
@@ -1,49 +1,5 @@
 #!/usr/bin/env nextflow
 
-//plotting for trimmed reads from ONT
-process nanoplot {
-    label "qc"
-    publishDir(
-        path: "${settings["outDir"]}/QcReads",
-        mode: 'copy'
-    )
-    input:
-    val settings
-    path unpaired
-
-    output:
-    path "*" //lots of output plots
-
-    script:
-    """
-    NanoPlot --fastq $unpaired --N50 --loglength -t ${settings["cpus"]} -f pdf --outdir . 2>/dev/null
-    """
-
-}
-
-
-//Porechop for removing adapters from ONT or PacBio reads
-process porechop {
-    label "qc"
-    publishDir(
-        path: "${settings["outDir"]}/QcReads",
-        mode: 'copy'
-    )
-
-
-    input:
-    val settings
-    path trimmed
-    path log
-    output:
-    path "*.porechop.fastq", emit: porechopped
-    
-    script:
-    """
-    porechop -i $trimmed -o ./QC.unpaired.porechop.fastq -t ${settings["cpus"]} > $log
-    """
-}
-
 //double-checks that any provided adapter file is in FASTA format
 process adapterFileCheck {
     label "qc"
@@ -60,8 +16,6 @@ process adapterFileCheck {
 }
 
 //main QC process. puts parameters together and runs FaQCs.
-//EDGE currently uses a custom script (illumina_fastq_QC.pl) to handle QC for long reads,
-//but it was unable to create report files when I attempted using it. For now, all input reads go through FaQCs.
 process qc {
     label "qc"
     publishDir(
@@ -71,8 +25,7 @@ process qc {
 
     input:
     val settings
-    path paired
-    path unpaired
+    path fastq
     val validAdapter
     path adapter
     val avgLen
@@ -86,20 +39,15 @@ process qc {
 
     script:
     //adjust minLength
-    def min = settings["minLength"]
-    if(settings["minLength"] < 1) {
-        min = Math.abs(settings["minLength"] * avgLen.toInteger())
+    def min = settings["minLen"]
+    if(settings["minLen"] < 1) {
+        min = Math.abs(settings["minLen"] * avgLen.toInteger())
     }
 
     def qcSoftware = "FaQCs"
-    // if(params.ontFlag || params.pacbioFlag) {
-    //     qcSoftware = "illumina_fastq_QC.pl"
-    // }
-    def pairedArg = paired.name != "NO_FILE" ? "-1 ${paired[0]} -2 ${paired[1]}" : ""
-    // if(pairedArg != "" && (params.ontFlag || params.pacbioFlag)) {
-    //     pairedArg = "-p $paired"
-    // }
-    def unpairedArg = unpaired.name != "NO_FILE2" ? "-u $unpaired" : ""
+
+    
+    def inputArg = settings["pairedFile"] ? "-1 ${fastq[0]} -2 ${fastq[1]}" : "-u $fastq"
 
     def adapterArg = ""
     if(adapter.name != "NO_FILE3" && validAdapter == "Yes"){
@@ -107,21 +55,16 @@ process qc {
     } 
 
     def polyA = settings["polyA"] ? "--polyA" : ""
-    def trim = ""
-    // if(params.ontFlag || params.pacbioFlag) {
-    //     trim = "--trim_only"
-    // }
-    def ascii = settings["phredOffset"] != null ? "--ascii ${settings["phredOffset"]}" : ""
+    def phiX = settings["filtPhiX"] ? "--phiX" : ""
 
     """
-    $qcSoftware $pairedArg $unpairedArg \
-    -q ${settings["qualityCutoff"]} --min_L $min --avg_q ${settings["avgQuality"]} \
-    -n ${settings["numN"]} --lc ${settings["lowComplexity"]} --5end ${settings["cut5end"]} --3end ${settings["cut3end"]} \
-    --split_size ${settings["splitSize"]} -d . -t ${settings["cpus"]} \
+    $qcSoftware $inputArg \
+    -q ${settings["trimQual"]} --min_L $min --avg_q ${settings["avgQual"]} \
+    -n ${settings["numN"]} --lc ${settings["filtLC"]} --5end ${settings["trim5end"]} --3end ${settings["trim3end"]} \
+    --split_size 1000000 -d . -t ${settings["cpus"]} \
     $polyA \
-    $trim \
     $adapterArg \
-    $ascii \
+    $phiX
     1>QC.log 2>&1
     """
 }
@@ -129,41 +72,32 @@ process qc {
 workflow FAQCS {
     take:
     settings
-    paired
-    unpaired
+    fastq
     avgLen
 
 
     main:
  
     //adapter setup
-    adapter_ch = channel.fromPath(settings["adapter"], checkIfExists:true)
+    adapter_ch = channel.fromPath(settings["artifactFile"], checkIfExists:true)
     //checks to see if the provided adapter file is a valid FASTA
     adapterFileCheck(adapter_ch)
 
     //main QC process
-    qc(settings, paired, unpaired, adapterFileCheck.out, adapter_ch, avgLen)
+    qc(settings, fastq, adapterFileCheck.out, adapter_ch, avgLen)
     
+
+    trimmed = channel.empty()
+    if(settings["pairedFile"]) {
+        trimmed = qc.out.pairedQC
+    }
+    else {
+        trimmed = qc.out.unpairedQC
+    }
     paired = qc.out.pairedQC
     unpaired = qc.out.unpairedQC
     
-    //long read trimming and plotting
-    if(settings["ontFlag"]) {
-        nanoplot_ch = channel.empty()
-        if(settings["porechop"]) {
-            porechop(settings, unpaired, qc.out.log)
-            nanoplot(settings, porechop.out.porechopped)
-            unpaired = porechop.out.porechopped
-        }
-        else {
-            nanoplot(settings, unpaired_ch)
-            unpaired = porechop.out.porechopped
-
-        }
-    }
-
     emit:
-    paired
-    unpaired
+    trimmed
 
 }
\ No newline at end of file
diff --git a/modules/sra2fastq/sra2fastq.nf b/modules/sra2fastq/sra2fastq.nf
index cac3000..04c03d1 100644
--- a/modules/sra2fastq/sra2fastq.nf
+++ b/modules/sra2fastq/sra2fastq.nf
@@ -1,5 +1,5 @@
 #!/usr/bin/env nextflow
-//to run: nextflow [OPT: -log /path/to/log file] run sra2fastq.nf -params-file [JSON parameter file]
+//to run: nextflow run sra2fastq.nf -params-file [JSON parameter file]
 //not supporting filesize or run count restrictions
 
 
@@ -9,7 +9,8 @@ process sraDownload {
     tag "$accession"
     publishDir "${settings["outDir"]}/SRA_Download", mode: 'copy'
 
-    //retries download in case of transient failure, then completes any processes that didn't fail
+    //retries download in case of transient failure, then completes any downloads that didn't fail
+
     maxRetries 3
     errorStrategy { (task.attempt <= maxRetries) ? 'retry' : 'finish' }
 
@@ -19,15 +20,14 @@ process sraDownload {
     val settings
 
     output:
-    path "$accession/${accession}.fastq.gz", emit: unpairedSRA, optional:true
-    path "$accession/${accession}_{1,2}.fastq.gz", emit: pairedSRA, optional:true
+    path "$accession/${accession}*.fastq.gz", emit: files
     path "$accession/${accession}_metadata.txt"
     path "$accession/sra2fastq_temp/*", optional: true //needed output?
 
     script: 
     //conditionally create command-line options based on non-empty parameters, for use in the command below
-    def clean = settings["clean"] != null ? "--clean True" : "" 
-    def platform_restrict = settings["platformRestrict"] != null ? "--platform_restrict ${settings["platformRestrict"]}" : ""
+    def clean = settings["clean"] ? "--clean True" : "" 
+    def platform_restrict = settings["fastqSource"] != null ? "--platform_restrict ${settings["fastqSource"]}" : ""
 
     //invoke sra2fastq.py with those options
     """
@@ -46,10 +46,9 @@ workflow SRA2FASTQ {
     accessions_ch = channel.of(settings["accessions"])
     sraDownload(accessions_ch.flatten().unique(), settings)
 
-    paired = sraDownload.out.pairedSRA
-    unpaired = sraDownload.out.unpairedSRA
+    fastq = sraDownload.out.files
 
     emit:
-    paired
-    unpaired
+    fastq
+
 }
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index d05751a..c1f8c17 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,12 +1,6 @@
 
 params {
 
-    //input
-    //pairedFiles = ["${projectDir}/nf_assets/NO_FILE"]
-    pairedFiles = ["${projectDir}/test_data/Ecoli_10x.1.fastq","${projectDir}/test_data/Ecoli_10x.2.fastq"]
-    unpairedFiles = ["${projectDir}/nf_assets/NO_FILE2"]
-    inputContigs = "${projectDir}/nf_assets/NO_FILE3"
-
     //which modules are run
     modules {
         sra2fastq = false
@@ -19,37 +13,34 @@ params {
     //module parameters -- passed directly into subworkflows according to best practices
     //these are the default values
     shared {
-        outDir = "./testing_output"
-        projName = "PROJECT"
+        inputFastq = null
+        inputContigs = "${projectDir}/nf_assets/NO_FILE3"
+        pairedFile = false
+        outDir = "EDGE_output"
+        projName = "Project"
         cpus = 8
-        fastqSource = "Illumina"
+        fastqSource = null
     }
 
     sra2fastq {
-        clean = null
-        platformRestrict = null
+        clean = false
+
         accessions = []
     }
 
     faqcs{
-        adapter = "${projectDir}/nf_assets/NO_FILE3"
-
-        qualityCutoff = 5
-        minLength = 50
-        avgQuality = 0
-        numN = 10
-        lowComplexity = 0.85
-        cut3end = 0
-        cut5end = 0
-        splitSize = 1000000
+        trimQual = 20
+        trim5end = 0
+        trim3end = 0
+        trimAdapter = false
+        trimPolyA = false
+        artifactFile = "${projectDir}/nf_assets/NO_FILE3"
+        minLen = 50
+        avgQual = 0
+        numN = 2
+        filtLC = 0.85
+        filtPhiX = false
 
-        ontFlag = false
-        pacbioFlag = false
-        polyA = false
-
-        phredOffset = null
-
-        porechop = false
     }
 
     hostRemoval {
@@ -152,3 +143,4 @@ executor {
 
 //cleanup
 cleanup = false
+
diff --git a/tests/modules/countFastq/countFastq.nf.test b/tests/modules/countFastq/countFastq.nf.test
index f2fe2ee..50759d1 100644
--- a/tests/modules/countFastq/countFastq.nf.test
+++ b/tests/modules/countFastq/countFastq.nf.test
@@ -8,11 +8,13 @@ nextflow_workflow {
 
         when {
             params {
-                // no special parameters
+                shared {
+                    pairedFile = false
+                }
             }
             workflow {
                 """
-                input[0] = file("${projectDir}/nf_assets/NO_FILE")
+                input[0] = params.shared
                 input[1] = file("${projectDir}/test_data/Ecoli_10x.1.fastq")
                 """
             }
@@ -33,38 +35,14 @@ nextflow_workflow {
 
         when {
             params {
-                // no special parameters
+                shared {
+                    pairedFile = true
+                }
             }
             workflow {
                 """
-                input[0] = [file("${projectDir}/test_data/Ecoli_10x.1.fastq"),file("${projectDir}/test_data/Ecoli_10x.2.fastq")]
-                input[1] = file("${projectDir}/nf_assets/NO_FILE2")
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                {assert workflow.success},
-                {assert snapshot(workflow.out).match()},
-                {assert workflow.out.avgReadLen.get(0) == "151"}
-            )
-            
-        }
-
-    }
-
-    
-    test("PE and SE files") {
-
-        when {
-            params {
-                // no special parameters
-            }
-            workflow {
-                """
-                input[0] = [file("${projectDir}/test_data/Ecoli_10x.1.fastq"),file("${projectDir}/test_data/Ecoli_10x.2.fastq")]
-                input[1] = file("${projectDir}/test_data/Ecoli_10x_copy.1.fastq")
+                input[0] = params.shared
+                input[1] = [file("${projectDir}/test_data/Ecoli_10x.1.fastq"),file("${projectDir}/test_data/Ecoli_10x.2.fastq")]
                 """
             }
         }
diff --git a/tests/modules/countFastq/countFastq.nf.test.snap b/tests/modules/countFastq/countFastq.nf.test.snap
index 17e1500..29758af 100644
--- a/tests/modules/countFastq/countFastq.nf.test.snap
+++ b/tests/modules/countFastq/countFastq.nf.test.snap
@@ -1,39 +1,4 @@
 {
-    "PE and SE files": {
-        "content": [
-            {
-                "0": [
-                    "151"
-                ],
-                "1": [
-                    [
-                        "all.1.fastq:md5,c9cd5b2586c75c7448674ff3ff5451de",
-                        "all.2.fastq:md5,3b69b59ed5c7111e5d57b900174ef2f6"
-                    ]
-                ],
-                "2": [
-                    "all.se.fastq:md5,c9cd5b2586c75c7448674ff3ff5451de"
-                ],
-                "avgReadLen": [
-                    "151"
-                ],
-                "paired": [
-                    [
-                        "all.1.fastq:md5,c9cd5b2586c75c7448674ff3ff5451de",
-                        "all.2.fastq:md5,3b69b59ed5c7111e5d57b900174ef2f6"
-                    ]
-                ],
-                "unpaired": [
-                    "all.se.fastq:md5,c9cd5b2586c75c7448674ff3ff5451de"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-10-28T13:16:37.86828"
-    },
     "1 Pair of PE files": {
         "content": [
             {
@@ -45,29 +10,24 @@
                         "all.1.fastq:md5,c9cd5b2586c75c7448674ff3ff5451de",
                         "all.2.fastq:md5,3b69b59ed5c7111e5d57b900174ef2f6"
                     ]
-                ],
-                "2": [
-                    
                 ],
                 "avgReadLen": [
                     "151"
                 ],
-                "paired": [
+                "fastqFiles": [
                     [
                         "all.1.fastq:md5,c9cd5b2586c75c7448674ff3ff5451de",
                         "all.2.fastq:md5,3b69b59ed5c7111e5d57b900174ef2f6"
                     ]
-                ],
-                "unpaired": [
-                    
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-28T13:18:00.975139"
+        "timestamp": "2025-01-06T13:53:45.128251613"
+
     },
     "1 Unpaired File": {
         "content": [
@@ -76,26 +36,22 @@
                     "151"
                 ],
                 "1": [
-                    
-                ],
-                "2": [
+
                     "all.se.fastq:md5,c9cd5b2586c75c7448674ff3ff5451de"
                 ],
                 "avgReadLen": [
                     "151"
                 ],
-                "paired": [
-                    
-                ],
-                "unpaired": [
+                "fastqFiles": [
+
                     "all.se.fastq:md5,c9cd5b2586c75c7448674ff3ff5451de"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-28T13:10:05.310905"
+        "timestamp": "2025-01-06T13:51:42.65748549"
     }
 }
\ No newline at end of file
diff --git a/tests/modules/runFaQCs/runFaQCs.nf.test b/tests/modules/runFaQCs/runFaQCs.nf.test
index 151fb2b..825b2ee 100644
--- a/tests/modules/runFaQCs/runFaQCs.nf.test
+++ b/tests/modules/runFaQCs/runFaQCs.nf.test
@@ -12,6 +12,7 @@ nextflow_workflow {
                     outDir = "./testing_output"
                     projName = "testFaQCs"
                     cpus = 4
+                    pairedFile = true
                 }
                 faqcs {
                     //all defaults
@@ -21,8 +22,7 @@ nextflow_workflow {
                 """
                 input[0] = params.faqcs.plus(params.shared)
                 input[1] = [file("${projectDir}/test_data/Ecoli_10x.1.fastq"),file("${projectDir}/test_data/Ecoli_10x.2.fastq")]
-                input[2] = file("${projectDir}/nf_assets/NO_FILE2")
-                input[3] = channel.of("151")
+                input[2] = channel.of("151")
                 """
             }
         }
@@ -42,6 +42,7 @@ nextflow_workflow {
                     outDir = "./testing_output"
                     projName = "testFaQCs"
                     cpus = 4
+                    pairedFile = false
                 }
                 faqcs {
                     //all defaults
@@ -50,72 +51,8 @@ nextflow_workflow {
             workflow {
                 """
                 input[0] = params.faqcs.plus(params.shared)
-                input[1] = [file("${projectDir}/nf_assets/NO_FILE")]
-                input[2] = file("${projectDir}/test_data/Ecoli_10x.1.fastq")
-                input[3] = channel.of("151")
-                """
-            }
-        }
-
-        then {
-            assert workflow.success
-            assert snapshot(workflow.out).match()
-        }
-
-    }
-
-    test("Nanopore SE (porechop/nanoplot)") {
-
-        when {
-            params {
-                shared {
-                    outDir = "./testing_output"
-                    projName = "testFaQCs"
-                    cpus = 4
-                }
-                faqcs {
-                    ontFlag = true
-                    porechop = true
-                }
-            }
-            workflow {
-                """
-                input[0] = params.faqcs.plus(params.shared)
-                input[1] = [file("${projectDir}/nf_assets/NO_FILE")]
-                input[2] = file("${projectDir}/test_data/Ecoli_10x.1.fastq")
-                input[3] = channel.of("151")
-                """
-            }
-        }
-
-        then {
-            assert workflow.success
-            assert snapshot(workflow.out).match()
-        }
-
-    }
-
-
-    test("PacBio SE (nanoplot)") {
-
-        when {
-            params {
-                shared {
-                    outDir = "./testing_output"
-                    projName = "testFaQCs"
-                    cpus = 4
-                }
-                faqcs {
-                    pacbioFlag = true
-                    porechop = true
-                }
-            }
-            workflow {
-                """
-                input[0] = params.faqcs.plus(params.shared)
-                input[1] = [file("${projectDir}/nf_assets/NO_FILE")]
-                input[2] = file("${projectDir}/test_data/Ecoli_10x.1.fastq")
-                input[3] = channel.of("151")
+                input[1] = file("${projectDir}/test_data/Ecoli_10x.1.fastq")
+                input[2] = channel.of("151")
                 """
             }
         }
@@ -135,17 +72,17 @@ nextflow_workflow {
                     outDir = "./testing_output"
                     projName = "testFaQCs"
                     cpus = 4
+                    pairedFile = true
                 }
                 faqcs {
-                    adapter = "${projectDir}/test_data/adapters.fasta"
+                    artifactFile = "${projectDir}/test_data/adapters.fasta"
                 }
             }
             workflow {
                 """
                 input[0] = params.faqcs.plus(params.shared)
                 input[1] = [file("${projectDir}/test_data/Ecoli_10x.1.fastq"),file("${projectDir}/test_data/Ecoli_10x.2.fastq")]
-                input[2] = file("${projectDir}/nf_assets/NO_FILE2")
-                input[3] = channel.of("151")
+                input[2] = channel.of("151")
                 """
             }
         }
@@ -165,17 +102,17 @@ nextflow_workflow {
                     outDir = "./testing_output"
                     projName = "testFaQCs"
                     cpus = 4
+                    pairedFile = false
                 }
                 faqcs {
-                    adapter = "${projectDir}/test_data/adapters.fasta"
+                    artifactFile = "${projectDir}/test_data/adapters.fasta"
                 }
             }
             workflow {
                 """
                 input[0] = params.faqcs.plus(params.shared)
-                input[1] = [file("${projectDir}/nf_assets/NO_FILE")]
-                input[2] = file("${projectDir}/test_data/Ecoli_10x.1.fastq")
-                input[3] = channel.of("151")
+                input[1] = file("${projectDir}/test_data/Ecoli_10x.1.fastq")
+                input[2] = channel.of("151")
                 """
             }
         }
@@ -195,6 +132,7 @@ nextflow_workflow {
                     outDir = "./testing_output"
                     projName = "testFaQCs"
                     cpus = 4
+                    pairedFile = true
                 }
                 faqcs {
                     polyA = true
@@ -204,8 +142,7 @@ nextflow_workflow {
                 """
                 input[0] = params.faqcs.plus(params.shared)
                 input[1] = [file("${projectDir}/test_data/Ecoli_10x.1.fastq"),file("${projectDir}/test_data/Ecoli_10x.2.fastq")]
-                input[2] = file("${projectDir}/nf_assets/NO_FILE2")
-                input[3] = channel.of("151")
+                input[2] = channel.of("151")
                 """
             }
         }
diff --git a/tests/modules/runFaQCs/runFaQCs.nf.test.snap b/tests/modules/runFaQCs/runFaQCs.nf.test.snap
index a2374bf..4b0c5df 100644
--- a/tests/modules/runFaQCs/runFaQCs.nf.test.snap
+++ b/tests/modules/runFaQCs/runFaQCs.nf.test.snap
@@ -1,181 +1,114 @@
 {
-    "Nanopore SE (porechop/nanoplot)": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    "QC.unpaired.porechop.fastq:md5,b8cdcb5e1eef7bdd518ef4e0a76dc63b"
-                ],
-                "paired": [
-                    
-                ],
-                "unpaired": [
-                    "QC.unpaired.porechop.fastq:md5,b8cdcb5e1eef7bdd518ef4e0a76dc63b"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-10-29T09:06:54.716065"
-    },
-    "PacBio SE (nanoplot)": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    "QC.unpaired.trimmed.fastq:md5,b8cdcb5e1eef7bdd518ef4e0a76dc63b"
-                ],
-                "paired": [
-                    
-                ],
-                "unpaired": [
-                    "QC.unpaired.trimmed.fastq:md5,b8cdcb5e1eef7bdd518ef4e0a76dc63b"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-10-29T09:19:41.968222"
-    },
     "PolyA removal": {
         "content": [
             {
                 "0": [
                     [
-                        "QC.1.trimmed.fastq:md5,eb49840329af7e3ed2d52cfb44d019d9",
-                        "QC.2.trimmed.fastq:md5,8dd551b2245f963ffe37b69018284501"
+                        "QC.1.trimmed.fastq:md5,deb773f1726c6134a7d2fc069af7b21b",
+                        "QC.2.trimmed.fastq:md5,a793e8ccfe60c0f9462a80d520eecd7a"
                     ]
                 ],
-                "1": [
-                    "QC.unpaired.trimmed.fastq:md5,d696a313f70f88a47f67c18cc75b683d"
-                ],
-                "paired": [
+                "trimmed": [
                     [
-                        "QC.1.trimmed.fastq:md5,eb49840329af7e3ed2d52cfb44d019d9",
-                        "QC.2.trimmed.fastq:md5,8dd551b2245f963ffe37b69018284501"
+                        "QC.1.trimmed.fastq:md5,deb773f1726c6134a7d2fc069af7b21b",
+                        "QC.2.trimmed.fastq:md5,a793e8ccfe60c0f9462a80d520eecd7a"
                     ]
-                ],
-                "unpaired": [
-                    "QC.unpaired.trimmed.fastq:md5,d696a313f70f88a47f67c18cc75b683d"
+
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-29T09:08:42.429862"
+        "timestamp": "2025-01-06T14:15:19.062459705"
+
     },
     "Basic SE": {
         "content": [
             {
                 "0": [
-                    
+                    "QC.unpaired.trimmed.fastq:md5,3a0138c06e9cd504e2cca8e5d93532f1"
                 ],
-                "1": [
-                    "QC.unpaired.trimmed.fastq:md5,b8cdcb5e1eef7bdd518ef4e0a76dc63b"
-                ],
-                "paired": [
-                    
-                ],
-                "unpaired": [
-                    "QC.unpaired.trimmed.fastq:md5,b8cdcb5e1eef7bdd518ef4e0a76dc63b"
+                "trimmed": [
+                    "QC.unpaired.trimmed.fastq:md5,3a0138c06e9cd504e2cca8e5d93532f1"
+
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-29T09:00:43.702411"
+        "timestamp": "2025-01-06T14:14:24.933787665"
+
     },
     "SE with adapter removal": {
         "content": [
             {
                 "0": [
-                    
-                ],
-                "1": [
-                    "QC.unpaired.trimmed.fastq:md5,83011948f673aac52bd300d247c2f6fa"
-                ],
-                "paired": [
-                    
+                    "QC.unpaired.trimmed.fastq:md5,3e43d37648eea875f5583f5cfcbb16ca"
                 ],
-                "unpaired": [
-                    "QC.unpaired.trimmed.fastq:md5,83011948f673aac52bd300d247c2f6fa"
+                "trimmed": [
+                    "QC.unpaired.trimmed.fastq:md5,3e43d37648eea875f5583f5cfcbb16ca"
+
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-29T09:08:11.110565"
+        "timestamp": "2025-01-06T14:15:03.845678151"
+
     },
     "Basic PE": {
         "content": [
             {
                 "0": [
                     [
-                        "QC.1.trimmed.fastq:md5,eb49840329af7e3ed2d52cfb44d019d9",
-                        "QC.2.trimmed.fastq:md5,8dd551b2245f963ffe37b69018284501"
+                        "QC.1.trimmed.fastq:md5,deb773f1726c6134a7d2fc069af7b21b",
+                        "QC.2.trimmed.fastq:md5,a793e8ccfe60c0f9462a80d520eecd7a"
                     ]
                 ],
-                "1": [
-                    "QC.unpaired.trimmed.fastq:md5,d696a313f70f88a47f67c18cc75b683d"
-                ],
-                "paired": [
+                "trimmed": [
                     [
-                        "QC.1.trimmed.fastq:md5,eb49840329af7e3ed2d52cfb44d019d9",
-                        "QC.2.trimmed.fastq:md5,8dd551b2245f963ffe37b69018284501"
+                        "QC.1.trimmed.fastq:md5,deb773f1726c6134a7d2fc069af7b21b",
+                        "QC.2.trimmed.fastq:md5,a793e8ccfe60c0f9462a80d520eecd7a"
                     ]
-                ],
-                "unpaired": [
-                    "QC.unpaired.trimmed.fastq:md5,d696a313f70f88a47f67c18cc75b683d"
+
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-28T14:51:51.359321"
+        "timestamp": "2025-01-06T14:14:13.196766924"
+
     },
     "PE with adapter removal": {
         "content": [
             {
                 "0": [
                     [
-                        "QC.1.trimmed.fastq:md5,d23266b2e5e5efdd1e086b54ce02f91b",
-                        "QC.2.trimmed.fastq:md5,5f79a0182d6cb56921a9318a060988b2"
+                        "QC.1.trimmed.fastq:md5,1e70223f29baaced4509b62a5e84f074",
+                        "QC.2.trimmed.fastq:md5,649bf376592b80e9ae1cee81d018a65f"
                     ]
                 ],
-                "1": [
-                    "QC.unpaired.trimmed.fastq:md5,d696a313f70f88a47f67c18cc75b683d"
-                ],
-                "paired": [
+                "trimmed": [
                     [
-                        "QC.1.trimmed.fastq:md5,d23266b2e5e5efdd1e086b54ce02f91b",
-                        "QC.2.trimmed.fastq:md5,5f79a0182d6cb56921a9318a060988b2"
+                        "QC.1.trimmed.fastq:md5,1e70223f29baaced4509b62a5e84f074",
+                        "QC.2.trimmed.fastq:md5,649bf376592b80e9ae1cee81d018a65f"
                     ]
-                ],
-                "unpaired": [
-                    "QC.unpaired.trimmed.fastq:md5,d696a313f70f88a47f67c18cc75b683d"
+
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-29T09:07:34.857606"
+        "timestamp": "2025-01-06T14:14:46.464717034"
     }
 }
\ No newline at end of file
diff --git a/tests/modules/sra2fastq/sra2fastq.nf.test b/tests/modules/sra2fastq/sra2fastq.nf.test
index 3e9b351..ddaf1a9 100644
--- a/tests/modules/sra2fastq/sra2fastq.nf.test
+++ b/tests/modules/sra2fastq/sra2fastq.nf.test
@@ -26,105 +26,13 @@ nextflow_workflow {
 
         then {
             assertAll(
-                {assert workflow.success },
-                {assert snapshot(workflow.out).match()}
-            )
-        }
-
-    }
-    
-    test("Ensure ILLUMINA platform") {
-
-        when {
-            params {
-                shared {
-                    outDir = "./testing_output"
-                    projName = "PROJECT"
-                    cpus = 4
-                }
-                sra2fastq {
-                    platformRestrict = "Illumina"
-                    accessions = ["SRR29462562"]
-                }
-            }
-            workflow {
-                """
-                input[0] = params.sra2fastq.plus(params.shared)
-                """
-            }
-        }
-
-        then {
-            assertAll (
                 {assert workflow.success},
                 {assert snapshot(workflow.out).match()}
             )
         }
 
     }
-
-    test("Ensure not PACBIO_SMRT platform") {
-
-        when {
-            params {
-                shared {
-                    outDir = "./testing_output"
-                    projName = "PROJECT"
-                    cpus = 4
-                }
-                sra2fastq {
-                    platformRestrict = "PACBIO_SMRT"
-                    accessions = ["SRR29462562"]
-                }
-            }
-            workflow {
-                """
-                input[0] = params.sra2fastq.plus(params.shared)
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                {assert workflow.success},
-                {assert workflow.out.paired.size() == 0},
-                {assert workflow.out.unpaired.size() == 0},
-                {assert snapshot(workflow.out).match()}
-            )
-        }
-
-    }
-    test("Ensure not OXFORD_NANOPORE platform") {
-
-        when {
-            params {
-                shared {
-                    outDir = "./testing_output"
-                    projName = "PROJECT"
-                    cpus = 4
-                }
-                sra2fastq {
-                    platformRestrict = "OXFORD_NANOPORE"
-                    accessions = ["SRR29462562"]
-                }
-            }
-            workflow {
-                """
-                input[0] = params.sra2fastq.plus(params.shared)
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                {assert workflow.success},
-                {assert workflow.out.paired.size() == 0},
-                {assert workflow.out.unpaired.size() == 0},
-                {assert snapshot(workflow.out).match()}
-            )
-        }
-
-    }
+    
     test("Only Download Unique Accessions") {
 
         when {
@@ -149,8 +57,7 @@ nextflow_workflow {
             assertAll (
                 {assert workflow.success},
                 {assert snapshot(workflow.out).match()},
-                {assert workflow.trace.succeeded().size() == 1},
-                {assert workflow.out.unpaired.size() == 1}
+                {assert workflow.out.fastq.size() == 1}
             )
         }
 
@@ -184,66 +91,4 @@ nextflow_workflow {
         }
 
     }
-    test("Multiple accessions") {
-
-        when {
-            params {
-                shared {
-                    outDir = "./testing_output"
-                    projName = "PROJECT"
-                    cpus = 4
-                }
-                sra2fastq {
-                    accessions = ["SRR11241255", "SRX20564104", "SRR29462562", "SRX24960352"]
-                    clean = true
-                }
-            }
-            workflow {
-                """
-                input[0] = params.sra2fastq.plus(params.shared)
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                {assert workflow.success},
-                {assert snapshot(workflow.out).match()},
-                {assert workflow.out.unpaired.size() == 2},
-                {assert workflow.out.paired.size() == 2}
-            )
-        }
-
-    }
-    test("Filtered Accessions") {
-
-        when {
-            params {
-                shared {
-                    outDir = "./testing_output"
-                    projName = "PROJECT"
-                    cpus = 4
-                }
-                sra2fastq {
-                    accessions = ["SRR11241255", "SRX20564104", "SRR29462562", "SRX24960352", "SRX26473729"]
-                    platformRestrict = "PACBIO_SMRT"
-                    clean = true
-                }
-            }
-            workflow {
-                """
-                input[0] = params.sra2fastq.plus(params.shared)
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                {assert workflow.success},
-                {assert snapshot(workflow.out).match()},
-                {assert workflow.out.unpaired.size() == 1}
-            )
-        }
-
-    }
 }
diff --git a/tests/modules/sra2fastq/sra2fastq.nf.test.snap b/tests/modules/sra2fastq/sra2fastq.nf.test.snap
index 0f091ec..dc8017c 100644
--- a/tests/modules/sra2fastq/sra2fastq.nf.test.snap
+++ b/tests/modules/sra2fastq/sra2fastq.nf.test.snap
@@ -1,202 +1,53 @@
 {
-    "Multiple accessions": {
-        "content": [
-            {
-                "0": [
-                    [
-                        "SRX20564104_1.fastq.gz:md5,4e4c4f89c097d782364f55a4828ba4c3",
-                        "SRX20564104_2.fastq.gz:md5,0a56586f63e03fc3c9d2cb26213b80f0"
-                    ],
-                    [
-                        "SRX24960352_1.fastq.gz:md5,e869779afbd424971f7e41aa342836cc",
-                        "SRX24960352_2.fastq.gz:md5,cb316c949fcb308017bbfe8ff5863752"
-                    ]
-                ],
-                "1": [
-                    "SRR11241255.fastq.gz:md5,2df0fa97a124de8b8d4d939f024bd594",
-                    "SRR29462562.fastq.gz:md5,31506ee0f339cb6398dd326d5cb23b77"
-                ],
-                "paired": [
-                    [
-                        "SRX20564104_1.fastq.gz:md5,4e4c4f89c097d782364f55a4828ba4c3",
-                        "SRX20564104_2.fastq.gz:md5,0a56586f63e03fc3c9d2cb26213b80f0"
-                    ],
-                    [
-                        "SRX24960352_1.fastq.gz:md5,e869779afbd424971f7e41aa342836cc",
-                        "SRX24960352_2.fastq.gz:md5,cb316c949fcb308017bbfe8ff5863752"
-                    ]
-                ],
-                "unpaired": [
-                    "SRR11241255.fastq.gz:md5,2df0fa97a124de8b8d4d939f024bd594",
-                    "SRR29462562.fastq.gz:md5,31506ee0f339cb6398dd326d5cb23b77"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-10-23T16:05:34.897015"
-    },
-    "Filtered Accessions": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    "SRX26473729.fastq.gz:md5,64e17afb49765db68336dbc9669f8a0d"
-                ],
-                "paired": [
-                    
-                ],
-                "unpaired": [
-                    "SRX26473729.fastq.gz:md5,64e17afb49765db68336dbc9669f8a0d"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-10-23T16:56:11.003119"
-    },
-    "Ensure not OXFORD_NANOPORE platform": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    
-                ],
-                "paired": [
-                    
-                ],
-                "unpaired": [
-                    
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-10-23T17:03:58.552875"
-    },
     "Only Download Unique Accessions": {
         "content": [
             {
                 "0": [
-                    
-                ],
-                "1": [
                     "SRR29462562.fastq.gz:md5,31506ee0f339cb6398dd326d5cb23b77"
                 ],
-                "paired": [
-                    
-                ],
-                "unpaired": [
+                "fastq": [
                     "SRR29462562.fastq.gz:md5,31506ee0f339cb6398dd326d5cb23b77"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-23T16:03:32.397274"
-    },
-    "Ensure ILLUMINA platform": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    "SRR29462562.fastq.gz:md5,31506ee0f339cb6398dd326d5cb23b77"
-                ],
-                "paired": [
-                    
-                ],
-                "unpaired": [
-                    "SRR29462562.fastq.gz:md5,31506ee0f339cb6398dd326d5cb23b77"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-10-23T16:01:45.248109"
-    },
-    "Ensure not PACBIO_SMRT platform": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    
-                ],
-                "paired": [
-                    
-                ],
-                "unpaired": [
-                    
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-10-23T17:03:47.363828"
+        "timestamp": "2025-01-06T17:32:54.040414641"
     },
     "Clean Output": {
         "content": [
             {
                 "0": [
-                    
-                ],
-                "1": [
                     "SRR29462562.fastq.gz:md5,31506ee0f339cb6398dd326d5cb23b77"
                 ],
-                "paired": [
-                    
-                ],
-                "unpaired": [
+                "fastq": [
                     "SRR29462562.fastq.gz:md5,31506ee0f339cb6398dd326d5cb23b77"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-23T16:04:16.360353"
+        "timestamp": "2025-01-06T17:33:53.778426755"
     },
     "Basic workflow": {
         "content": [
             {
                 "0": [
-                    
-                ],
-                "1": [
                     "SRR29462562.fastq.gz:md5,31506ee0f339cb6398dd326d5cb23b77"
                 ],
-                "paired": [
-                    
-                ],
-                "unpaired": [
+                "fastq": [
                     "SRR29462562.fastq.gz:md5,31506ee0f339cb6398dd326d5cb23b77"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-23T16:01:03.780856"
+        "timestamp": "2025-01-06T18:04:07.033920358"
     }
 }
\ No newline at end of file
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 7e7ba26..77b6402 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -4,4 +4,5 @@
 ========================================================================================
 */
 
-cleanup = false
\ No newline at end of file
+cleanup = false //necessary to compare snapshotted files
+