diff --git a/bin/freec_paired.pl b/bin/make_freec_genome_paired.pl
similarity index 95%
rename from bin/freec_paired.pl
rename to bin/make_freec_genome_paired.pl
index 161e24e..474dfaf 100644
--- a/bin/freec_paired.pl
+++ b/bin/make_freec_genome_paired.pl
@@ -26,18 +26,19 @@
 print C "chrFiles = $chrFiles\n";
 print C "minimalSubclonePresence = 20\nmaxThreads = 8\n";
 print C "outputDir = $ARGV[0]\n\n";
- 
+
 print C '[sample]' . "\n\n";
- 
+
 print C "mateFile = $tumormateFile\n";
 print C "inputFormat = BAM\nmateOrientation = FR\n\n";
 
-print C '[BAF]' . "\n\n";
+print C '[control]' . "\n\n";
 
 print C "mateFile = $controlmateFile\n";
 print C "inputFormat = BAM\nmateOrientation = FR\n\n";
- 
+
+print C '[BAF]' . "\n\n";
 print C "makePileup = $makePileup\n";
 print C "fastaFile = $fastaFile\n";
 print C "minimalCoveragePerPosition = 20\nminimalQualityPerPosition = 20\n";
-print C "SNPfile = $SNPfile";
+print C "SNPfile = $SNPfile";
\ No newline at end of file
diff --git a/conf/base.config b/conf/base.config
index c525125..0eb1dee 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -51,6 +51,21 @@ process {
     withLabel:process_high_memory {
         memory = { check_max( 200.GB * task.attempt, 'memory' ) }
     }
+    withLabel:process_somaticcaller {
+        cpus   = { check_max( 4     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 64.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 72.h   * task.attempt, 'time'    ) }
+    }
+    withLabel:process_somaticcaller_high {
+        cpus   = { check_max( 16     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 70.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 48.h   * task.attempt, 'time'    ) }
+    }
+    withLabel:process_highmem {
+        cpus   = { check_max( 4     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 48.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 72.h   * task.attempt, 'time'    ) }
+    }
     withLabel:error_ignore {
         errorStrategy = 'ignore'
     }
@@ -58,4 +73,5 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
+
 }
diff --git a/conf/biowulf.config b/conf/biowulf.config
index a679cf1..77a06d5 100644
--- a/conf/biowulf.config
+++ b/conf/biowulf.config
@@ -22,7 +22,7 @@ singularity {
     autoMounts = true
     cacheDir = "/data/CCBR_Pipeliner/SIFS"
     envWhitelist = 'https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOBID,SINGULARITY_BINDPATH'
-    runOptions = '-B /gs10,/gs11,/gs12,/gs9,/spin1,/data/CCBR_Pipeliner/,/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/,/data/nousomedr/,/data/CCBR/projects/,/vf/users,/gpfs,/fdb'
+    runOptions = '-B /gs10,/gs11,/gs12,/gs9,/spin1,/data/CCBR_Pipeliner/,/data/CCBR/projects/,/vf/users,/gpfs,/fdb'
 }
 
 env.SINGULARITY_CACHEDIR = "/data/CCBR_Pipeliner/SIFS"
@@ -34,4 +34,4 @@ process {
     stageOutMode = 'rsync'
     // for running pipeline on group sharing data directory, this can avoid inconsistent files timestamps
     cache = 'lenient'
-}
\ No newline at end of file
+}
diff --git a/conf/containers.config b/conf/containers.config
index 504d3b8..2ceaf3c 100644
--- a/conf/containers.config
+++ b/conf/containers.config
@@ -2,6 +2,9 @@
 params {
     containers {
         base = 'nciccbr/ccbr_ubuntu_base_20.04:v6.1'
-        logan = 'docker://dnousome/ccbr_logan_base:v0.3.0' 
+        logan = 'docker://dnousome/ccbr_logan_base:v0.3.3'
+        vcf2maf = 'docker://dnousome/ccbr_vcf2maf:v102.0.0'
+        octopus = 'docker://dancooke/octopus:latest'
+
     }
 }
diff --git a/conf/genomes.config b/conf/genomes.config
index 2ee6cdc..3d0843a 100644
--- a/conf/genomes.config
+++ b/conf/genomes.config
@@ -1,11 +1,11 @@
 params {
     genomes {
         'hg38' {
-            genome = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/bwamem2/Homo_sapiens_assembly38.fasta" 
-            genomefai = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/bwamem2/Homo_sapiens_assembly38.fasta.fai" 
+            genome = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/bwamem2/Homo_sapiens_assembly38.fasta"
+            genomefai = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/bwamem2/Homo_sapiens_assembly38.fasta.fai"
             bwagenome= "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/genome/Homo_sapiens_assembly38.fasta"
             genomedict= "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/genome/Homo_sapiens_assembly38.dict"
-            wgsregion = "/data/nousomedr/annotation/resources_broad_hg38_v0_wgs_calling_regions.hg38.interval_list" 
+            wgsregion = "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/resources_broad_hg38_v0_wgs_calling_regions.hg38.interval_list"
             intervals= "${projectDir}/assets/hg38_v0_wgs_calling_regions.hg38.bed"
             //millsindel = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz" //Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
             //shapeitindel =  "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz" //ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz" //file(params.gold_indels2) //
@@ -14,7 +14,7 @@ params {
             dbsnp = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/dbsnp_138.hg38.vcf.gz"
             dbsnp_indel = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/dbsnp_indel.vcf"
             gnomad = '--germline-resource /data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GNOMAD/somatic-hg38-af-only-gnomad.hg38.vcf.gz' // /data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GNOMAD/somatic-hg38-af-only-gnomad.hg38.vcf.gz
-            pon = "/data/nousomedr/wgs/updatedpon.vcf.gz"    //pon="/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/PON/hg38.noCOSMIC_ClinVar.pon.vcf.gz" //file{params.pon} 
+            pon = "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/PON/updatedpon.vcf.gz"    //pon="/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/PON/hg38.noCOSMIC_ClinVar.pon.vcf.gz" //file{params.pon}
             kgp = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz"
             KRAKENBACDB = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/kraken/20180907_standard_kraken2"
             snpeff_genome = "GRCh38.86"
@@ -29,11 +29,11 @@ params {
             octopus_gforest= "--forest /data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/octopus/germline.v0.7.4.forest"
             SEQUENZAGC = "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/SEQUENZA/hg38_gc50Base.txt.gz"
             chromosomes = ['chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9','chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17','chr18','chr19','chr20','chr21','chr22','chrX','chrY','chrM']
-        }    
+        }
 
         'mm10' {
-            genome = "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/genome/bwamem2index/genome.fa" // file(params.genome) 
-            genomefai = "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/genome/bwamem2index/genome.fa.fai" // file(params.genome) 
+            genome = "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/genome/bwamem2index/genome.fa" // file(params.genome)
+            genomefai = "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/genome/bwamem2index/genome.fa.fai" // file(params.genome)
             bwagenome= "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/genome/bwaindex/genome.fa"
             genomedict= "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/genome/bwamem2index/genome.dict"
             intervals="/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/genome/bwamem2index/mm10_wgsregions.bed"
@@ -66,6 +66,3 @@ params {
         }
     }
 }
-
-
-
diff --git a/conf/interactive.config b/conf/interactive.config
index 725d1ae..9808cb5 100644
--- a/conf/interactive.config
+++ b/conf/interactive.config
@@ -4,7 +4,7 @@ params {
     max_cpus = 56
     max_time = '12 h'
 
-    
+
 }
 process.scratch = false
 
@@ -14,4 +14,6 @@ singularity {
     autoMounts = true
     cacheDir = "/data/CCBR_Pipeliner/SIFS"
     envWhitelist='https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOBID,SINGULARITY_BINDPATH'
-}
\ No newline at end of file
+}
+
+env.SINGULARITY_CACHEDIR = "/data/CCBR_Pipeliner/SIFS"
diff --git a/conf/modules.config b/conf/modules.config
index 4c3522c..d171cef 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -9,27 +9,22 @@ process {
     errorStrategy = 'finish'
 
     withName:'sequenza' {
-        container = 'dnousome/ccbr_logan_base:v0.3.0'
         publishDir = [
             path: { "${params.outdir}/cnv/sequenza" },
             mode: 'copy'
         ]
     }
 
-
     withName: 'freec_paired' {
         publishDir = [
-            path: { "${params.outdir}/cnv/freec" },
+            path: { "${params.outdir}/cnv/freec_paired" },
             mode: 'copy'
         ]
-        container = 'dnousome/ccbr_logan_base:v0.3.0' 
-
     }
 
-    withName:'freec' {
-        container = 'dnousome/ccbr_logan_base:v0.3.0' 
+    withName: 'freec' {
         publishDir = [
-            path: { "${params.outdir}/cnv/freec" },
+            path: { "${params.outdir}/cnv/freec_unpaired" },
             mode: 'copy'
         ]
     }
@@ -192,7 +187,7 @@ process {
             mode: 'copy'
         ]
     }
-      
+
     withName: 'annotsv_tn' {
         publishDir = [
             path: { "${params.outdir}/SV/annotated" },
@@ -291,5 +286,6 @@ process {
             path: { "${params.outdir}/vcfs/combined" },
             mode: 'copy'
         ]
-    }   
+    }
+
 }
diff --git a/main.nf b/main.nf
index f2c2802..0a715e1 100644
--- a/main.nf
+++ b/main.nf
@@ -5,14 +5,12 @@ date = new Date().format( 'yyyyMMdd' )
 
 
 log.info """\
-         L O G A N     P I P E L I N E    
+         L O G A N     P I P E L I N E
          =============================
          genome: ${params.genome}
          outdir: ${params.outdir}
          Sample Sheet: ${params.sample_sheet}
-         Samples: ${params.fastq_input} ${params.file_input} ${params.bam_input}
-         NF version   : $nextflow.version
-
+         Samples: ${params.fastq_input} ${params.fastq_file_input} ${params.bam_input} ${params.bam_file_input}
          """
          .stripIndent()
 
@@ -40,8 +38,7 @@ workflow.onComplete {
 
 //Final Workflow
 workflow {
-    DETERMINEBAM()
-    if ([params.fastq_input,params.file_input].any() && params.sample_sheet && !params.BAMINPUT){
+        if ([params.fastq_input,params.fastq_file_input].any() && params.sample_sheet){
         println "Tumor-Normal FASTQ"
         INPUT()
         ALIGN(INPUT.out.fastqinput,INPUT.out.sample_sheet)
@@ -52,10 +49,10 @@ workflow {
         //Tumor-Normal VC, SV, CNV
         if (params.vc){
             VC(ALIGN.out.bamwithsample,ALIGN.out.splitout,ALIGN.out.sample_sheet)
-        }   
+        }
         if (params.sv){
             SV(ALIGN.out.bamwithsample)
-        }  
+        }
         if (params.cnv){
             if (params.genome == "mm10"){
                 CNVmouse(ALIGN.out.bamwithsample)
@@ -67,25 +64,25 @@ workflow {
                     CNVhuman(ALIGN.out.bamwithsample,VC.out.somaticcall_input)
                 }
             }
-    }  
+    }
         if (params.qc && params.gl){
             QC_GL(ALIGN.out.fastqin,ALIGN.out.fastpout,ALIGN.out.bqsrout,GL.out.glnexusout,GL.out.bcfout)
         }  else if (params.qc){
             QC_NOGL(ALIGN.out.fastqin,ALIGN.out.fastpout,ALIGN.out.bqsrout)
-        }  
+        }
 
     }
-    
+
     //TUMOR-NOMRAL BAM INPUT
-    if ([params.bam_input,params.file_input].any() && params.sample_sheet && BAMINPUT){
+    if ([params.bam_input,params.bam_file_input].any() && params.sample_sheet){
         println "Tumor-Normal with BAMs"
         INPUT_BAM()
         if (params.vc){
             VC(INPUT_BAM.out.bamwithsample,INPUT_BAM.out.splitout,INPUT_BAM.out.sample_sheet)
-        }  
+        }
         if (params.sv){
             SV(INPUT_BAM.out.bamwithsample)
-        }  
+        }
         if (params.cnv){
             if (params.genome == "mm10"){
                 CNVmouse(INPUT_BAM.out.bamwithsample)
@@ -93,15 +90,15 @@ workflow {
                 if (!params.vc){
                     VC(INPUT_BAM.out.bamwithsample,INPUT_BAM.out.splitout,INPUT_BAM.out.sample_sheet)
                     CNVhuman(INPUT_BAM.out.bamwithsample,VC.out.somaticcall_input)
-                }else { 
+                }else {
                     CNVhuman(INPUT_BAM.out.bamwithsample,VC.out.somaticcall_input)
                 }
             }
         }
-    }  
-    
+    }
+
     ///Tumor Only Pipelines
-    if ([params.fastq_input,params.file_input].any() && !params.sample_sheet && !params.BAMINPUT){
+    if ([params.fastq_input,params.file_input].any() && !params.sample_sheet){
         println "Tumor-Only FASTQ"
         INPUT_TONLY()
         ALIGN_TONLY(INPUT_TONLY.out.fastqinput,INPUT_TONLY.out.sample_sheet)
@@ -118,7 +115,7 @@ workflow {
                 if (!params.vc){
                     VC_TONLY(ALIGN_TONLY.out.bamwithsample,ALIGN_TONLY.out.splitout,ALIGN_TONLY.out.sample_sheet)
                     CNVhuman_tonly(ALIGN_TONLY.out.bamwithsample,VC_TONLY.out.somaticcall_input)
-                } else{
+                } else {
                     CNVhuman_tonly(ALIGN_TONLY.out.bamwithsample,VC_TONLY.out.somaticcall_input)
                 }
             }
@@ -129,7 +126,7 @@ workflow {
     }
 
     //Variant Calling from BAM-Tumor Only Mode
-    if ([params.bam_input,params.file_input].any() && !params.sample_sheet && params.BAMINPUT){
+    if ([params.bam_input,params.bam_file_input].any() && !params.sample_sheet){
         println "Tumor-Only BAM"
         INPUT_TONLY_BAM()
         if (params.vc){
@@ -137,20 +134,19 @@ workflow {
         }
         if (params.sv){
             SV_TONLY(INPUT_TONLY_BAM.out.bamwithsample)
-        }  
+        }
         if (params.cnv){
             if (params.genome == "mm10"){
                 CNVmouse_tonly(INPUT_TONLY_BAM.out.bamwithsample)
             } else if (params.genome== "hg38"){
-                VC_TONLY(INPUT_TONLY_BAM.out.bamwithsample,INPUT_TONLY_BAM.out.splitout,INPUT_TONLY_BAM.out.sample_sheet)
-                CNVhuman_tonly(INPUT_TONLY_BAM.out.bamwithsample,VC_TONLY.out.somaticcall_input)
-            }
-        }  
-    
-    }
+                if (!params.vc){
+                    VC_TONLY(INPUT_TONLY_BAM.out.bamwithsample,INPUT_TONLY_BAM.out.splitout,INPUT_TONLY_BAM.out.sample_sheet)
+                    CNVhuman_tonly(INPUT_TONLY_BAM.out.bamwithsample,VC_TONLY.out.somaticcall_input)
+                } else {
+                    CNVhuman_tonly(INPUT_TONLY_BAM.out.bamwithsample,VC_TONLY.out.somaticcall_input)
+                }
 
+        }
+        }
+    }
 }
-
-    
-
-
diff --git a/modules/local/copynumber.nf b/modules/local/copynumber.nf
index 757465a..0f4a92b 100644
--- a/modules/local/copynumber.nf
+++ b/modules/local/copynumber.nf
@@ -21,12 +21,13 @@ ENSEMBLCACHE='/data/SCLC-BRAINMETS/cn/common/ensembl_data'
 DRIVERS='/data/SCLC-BRAINMETS/cn/common/DriverGenePanel.38.tsv'
 HOTSPOTS='/data/SCLC-BRAINMETS/cn/variants/KnownHotspots.somatic.38.vcf.gz'
 
-//DBSNP_INDEL=file(params.genomes[params.genome].KNOWNINDELS) 
+//DBSNP_INDEL=file(params.genomes[params.genome].KNOWNINDELS)
 //ascatR=
 
 
-//mm10 Paired-Sequenza, FREEC-tumor only 
+//mm10 Paired-Sequenza, FREEC-tumor only
 process seqz_sequenza_bychr {
+    container = "${params.containers.logan}"
     label 'process_low'
 
     input:
@@ -57,13 +58,15 @@ process seqz_sequenza_bychr {
 
 
 process sequenza {
+    container = "${params.containers.logan}"
+
     label 'process_highcpu'
 
     input:
         tuple val(pairid), path(seqz)
 
     output:
-        tuple val(pairid), 
+        tuple val(pairid),
         path("${pairid}_alternative_solutions.txt"),
         path("${pairid}_alternative_fit.pdf"),
         path("${pairid}_model_fit.pdf"),
@@ -83,9 +86,9 @@ process sequenza {
     //samtools mpileup ${normal} -f $GENOMEREF -Q 20 |gzip > ${normalname}.mpileup.gz
     //sequenza-utils seqz_binning --seqz --window 50 -o ${sample}_bin50.seqz.gz
 
-    shell: 
+    shell:
     '''
-    
+
     zcat !{seqz} | awk '{if (NR==1) {print $0} else {if ($1!="chromosome"){print $0}}}' |\
     sequenza-utils seqz_binning \
         -w 100 \
@@ -99,11 +102,11 @@ process sequenza {
 
     '''
 
-    stub: 
-    
+    stub:
+
     """
-    touch "${pairid}_alternative_solutions.txt" 
-    touch "${pairid}_alternative_fit.pdf" 
+    touch "${pairid}_alternative_solutions.txt"
+    touch "${pairid}_alternative_fit.pdf"
     touch "${pairid}_model_fit.pdf"
     touch "${pairid}_confints_CP.txt"
     touch "${pairid}_CN_bars.pdf"
@@ -121,13 +124,25 @@ process sequenza {
 
 }
 
+
 process freec_paired {
+    container = "${params.containers.logan}"
     label 'process_highcpu'
 
     input:
-        tuple val(tumorname), path(tumor), path(tumorbai), val(normalname), path(normal), path(normalbai)
+        tuple val(tumorname), path(tumor), path(tumorbai),
+        val(normalname), path(normal), path(normalbai)
 
-    shell: """
+    output:
+        tuple val(tumorname), val(normalname),
+        path("${tumorname}_vs_${normalname}_CNVs.p.value.txt"),
+        path("${tumorname}_vs_${normalname}_ratio.txt"),
+        path("${tumorname}_vs_${normalname}_BAF.txt"),
+        path("${tumorname}_vs_${normalname}_ratio.txt.log2.png"),
+        path("${tumorname}_vs_${normalname}_ratio.txt.png")
+
+    shell:
+    """
 
     perl $FREECPAIR_SCRIPT \
         . \
@@ -150,29 +165,47 @@ process freec_paired {
     cat $FREECPLOT | \
         R --slave \
         --args 2 \
-        ${tumorname}_vs_${normalname}.bam_ratio.txt \
-        ${tumorname}_vs_${normalname}.bam_BAF.txt
+        ${tumor}_ratio.txt \
+        ${tumor}_BAF.txt
+
+    mv ${tumor}_CNVs.p.value.txt ${tumorname}_vs_${normalname}_CNVs.p.value.txt
+    mv ${tumor}_ratio.txt ${tumorname}_vs_${normalname}_ratio.txt
+    mv ${tumor}_BAF.txt ${tumorname}_vs_${normalname}_BAF.txt
+    mv ${tumor}_BAF.txt.png ${tumorname}_vs_${normalname}_BAF.txt.png
+    mv ${tumor}_ratio.txt.log2.png ${tumorname}_vs_${normalname}_ratio.txt.log2.png
+    mv ${tumor}_ratio.txt.png ${tumorname}_vs_${normalname}_ratio.txt.png
 
-    """      
+    """
 
     stub:
     """
-    touch ${tumorname}_vs_${normalname}.bam_CNVs.p.value.txt  
-    touch ${tumorname}_vs_${normalname}.bam_ratio.txt 
-    touch ${tumorname}_vs_${normalname}.bam_BAF.txt
-    touch ${tumorname}_vs_${normalname}.bam_ratio.txt.log2.png
-    touch ${tumorname}_vs_${normalname}.bam_ratio.txt.png
+    touch ${tumorname}_vs_${normalname}_CNVs.p.value.txt
+    touch ${tumorname}_vs_${normalname}_ratio.txt
+    touch ${tumorname}_vs_${normalname}_BAF.txt
+    touch ${tumorname}_vs_${normalname}_BAF.txt.png
+    touch ${tumorname}_vs_${normalname}_ratio.txt.log2.png
+    touch ${tumorname}_vs_${normalname}_ratio.txt.png
 
     """
 }
 
 
 process freec {
-    label 'process_mid'
+    container = "${params.containers.logan}"
+    label 'process_medium'
 
     input:
         tuple val(tumorname), path(tumor), path(tumorbai)
 
+    output:
+        tuple val(tumorname),
+        path("${tumorname}_CNVs.p.value.txt"),
+        path("${tumorname}_ratio.txt"),
+        path("${tumorname}_BAF.txt"),
+        path("${tumorname}_ratio.txt.log2.png"),
+        path("${tumorname}_ratio.txt.png")
+
+
     shell: """
 
     perl $FREECSCRIPT \
@@ -198,26 +231,36 @@ process freec {
         ${tumor}_ratio.txt \
         ${tumor}_BAF.txt
 
-    """      
+    mv ${tumor}_CNVs.p.value.txt ${tumorname}_CNVs.p.value.txt
+    mv ${tumor}_ratio.txt ${tumorname}_ratio.txt
+    mv ${tumor}_BAF.txt ${tumorname}_BAF.txt
+    mv ${tumor}_BAF.txt.png ${tumorname}_BAF.txt.png
+    mv ${tumor}_ratio.txt.log2.png ${tumorname}_ratio.txt.log2.png
+    mv ${tumor}_ratio.txt.png ${tumorname}_ratio.txt.png
+
+    """
 
     stub:
     """
-    touch ${tumor}_CNVs.p.value.txt  
-    touch ${tumor}_ratio.txt 
-    touch ${tumor}_BAF.txt 
-    touch ${tumor}_ratio.txt.log2.png
-    touch ${tumor}_ratio.txt.png
+    touch ${tumorname}_CNVs.p.value.txt
+    touch ${tumorname}_ratio.txt
+    touch ${tumorname}_BAF.txt
+    touch ${tumorname}_BAF.txt.png
+    touch ${tumorname}_ratio.txt.log2.png
+    touch ${tumorname}_ratio.txt.png
 
     """
 }
 
 
 process amber_tonly {
-    label 'process_mid'
+    container = "${params.containers.logan}"
+
+    label 'process_medium'
 
     input:
         tuple val(tumorname), path(tumor), path(tumorbai)
-       
+
 
     output:
         tuple val(tumorname), path("${tumorname}_amber")
@@ -243,13 +286,15 @@ process amber_tonly {
 
     """
     mkdir ${tumorname}_amber
-    touch ${tumorname}_amber/${tumorname}.amber.baf.tsv.gz ${tumorname}_amber/${tumorname}.amber.baf.pcf ${tumorname}_amber/${tumorname}.amber.qc 
+    touch ${tumorname}_amber/${tumorname}.amber.baf.tsv.gz ${tumorname}_amber/${tumorname}.amber.baf.pcf ${tumorname}_amber/${tumorname}.amber.qc
     """
 }
 
 process amber_tn {
-    label 'process_mid'
-    
+    container = "${params.containers.logan}"
+
+    label 'process_medium'
+
     input:
         tuple val(tumorname), path(tumor), path(tumorbai),
         val(normalname), path(normal), path(normalbai)
@@ -279,19 +324,21 @@ process amber_tn {
 
     """
     mkdir ${tumorname}_vs_${normalname}_amber
-    touch ${tumorname}_vs_${normalname}_amber/${tumorname}.amber.baf.tsv.gz ${tumorname}_vs_${normalname}_amber/${tumorname}.amber.baf.pcf ${tumorname}_vs_${normalname}_amber/${tumorname}.amber.qc 
+    touch ${tumorname}_vs_${normalname}_amber/${tumorname}.amber.baf.tsv.gz ${tumorname}_vs_${normalname}_amber/${tumorname}.amber.baf.pcf ${tumorname}_vs_${normalname}_amber/${tumorname}.amber.qc
     """
 }
 
 process cobalt_tonly {
-    label "process_mid"
+    container = "${params.containers.logan}"
+
+    label 'process_medium'
 
     input:
         tuple val(tumorname), path(tumor), path(tumorbai)
 
     output:
         tuple val(tumorname), path("${tumorname}_cobalt")
-        //path("${samplename}/${samplename}.cobalt.ratio.tsv.gz"), 
+        //path("${samplename}/${samplename}.cobalt.ratio.tsv.gz"),
         //path("${samplename}/${samplename}.cobalt.ratio.pcf"),
         //path("${samplename}/${samplename}.cobalt.gc.median.tsv")
 
@@ -317,7 +364,9 @@ process cobalt_tonly {
 }
 
 process cobalt_tn {
-    label "process_mid"
+    container = "${params.containers.logan}"
+
+    label 'process_medium'
 
     input:
         tuple val(tumorname), path(tumor), path(tumorbai),
@@ -325,7 +374,7 @@ process cobalt_tn {
 
     output:
         tuple val(tumorname), path("${tumorname}_vs_${normalname}_cobalt")
-        //path("${samplename}/${samplename}.cobalt.ratio.tsv.gz"), 
+        //path("${samplename}/${samplename}.cobalt.ratio.tsv.gz"),
         //path("${samplename}/${samplename}.cobalt.ratio.pcf"),
         //path("${samplename}/${samplename}.cobalt.gc.median.tsv")
 
@@ -353,12 +402,12 @@ process cobalt_tn {
 
 
 process purple {
-    label 'process_mid'
-    publishDir("${outdir}/cnv/purple", mode: 'copy')
+    container = "${params.containers.logan}"
+    label 'process_medium'
 
     input:
         tuple val(tumorname),
-        path(cobaltin), 
+        path(cobaltin),
         path(amberin),
         path(somaticvcf),
         path(somaticvcfindex)
@@ -396,8 +445,6 @@ process purple {
 process ascat_tn {
     module=["java/12.0.1","R/3.6.3"]
 
-    publishDir("${outdir}/purple", mode: 'copy')
-
     input:
         tuple val(samplename), path(cobaltin), path(amberin), path("${samplename}.tonly.final.mut2.vcf.gz")
 
@@ -436,4 +483,3 @@ process ascat_tn {
 }
 
 */
-
diff --git a/modules/local/germline.nf b/modules/local/germline.nf
index c106683..285a0f3 100644
--- a/modules/local/germline.nf
+++ b/modules/local/germline.nf
@@ -5,15 +5,15 @@ MODEL="/opt/models/wgs/model.ckpt"
 //Processes
 //Deep Variant
 process deepvariant_step1 {
-    
+
     input:
         tuple val(samplename), path("${samplename}.bam"), path("${samplename}.bai"), path(bed)
-    
+
     output:
-        tuple val(samplename), path("outputshard/${samplename}.tfrecord_${bed}.gz"), 
+        tuple val(samplename), path("outputshard/${samplename}.tfrecord_${bed}.gz"),
         path("gvcf/${samplename}.gvcf.tfrecord_${bed}.gz")
 
-    script:     
+    script:
     """
     mkdir -p outputshard
     mkdir -p gvcf
@@ -24,7 +24,7 @@ process deepvariant_step1 {
     --reads ${samplename}.bam \
     --channels insert_size \
     --examples outputshard/${samplename}.tfrecord_${bed}.gz \
-    --gvcf gvcf/${samplename}.gvcf.tfrecord_${bed}.gz 
+    --gvcf gvcf/${samplename}.gvcf.tfrecord_${bed}.gz
     """
 
     stub:
@@ -32,23 +32,22 @@ process deepvariant_step1 {
     mkdir -p outputshard
     mkdir -p gvcf
     touch outputshard/${samplename}.tfrecord_${bed}.gz
-    touch gvcf/${samplename}.gvcf.tfrecord_${bed}.gz 
+    touch gvcf/${samplename}.gvcf.tfrecord_${bed}.gz
     """
 
 }
 
 //Step 2 requires GPU
 process deepvariant_step2 {
-    
-    
+
     input:
         tuple val(samplename), path(tfrecords), path(tfgvcf)
-    
+
     output:
-        tuple val(samplename), path(tfrecords), 
+        tuple val(samplename), path(tfrecords),
         path("${samplename}_call_variants_output.tfrecord.gz"), path(tfgvcf)
 
-    script: 
+    script:
 
     """
     call_variants \
@@ -69,17 +68,16 @@ process deepvariant_step2 {
 //Step 3 DV
 process deepvariant_step3 {
 
-    
     input:
         tuple val(samplename), path(tfrecords), path("${samplename}_call_variants_output.tfrecord.gz"),
         path(tfgvcf)
-    
+
     output:
         tuple val(samplename), path("${samplename}.vcf.gz"), path("${samplename}.vcf.gz.tbi"),
         path("${samplename}.gvcf.gz"), path("${samplename}.gvcf.gz.tbi")
 
 
-    script: 
+    script:
     """
    postprocess_variants \
     --ref $GENOMEREF \
@@ -101,16 +99,15 @@ process deepvariant_step3 {
 //Combined DeepVariant
 process deepvariant_combined {
 
-
     input:
         tuple val(samplename), path("${samplename}.bam"), path("${samplename}.bai")
-    
+
     output:
         tuple val(samplename), path("${samplename}.gvcf.gz"), path("${samplename}.gvcf.gz.tbi"),
         path("${samplename}.vcf.gz"), path("${samplename}.vcf.gz.tbi")
 
 
-    script:     
+    script:
     """
     run_deepvariant \
         --model_type=WGS \
@@ -118,7 +115,7 @@ process deepvariant_combined {
         --reads=${samplename}.bam \
         --output_gvcf= ${samplename}.gvcf.gz \
         --output_vcf=${samplename}.vcf.gz \
-        --num_shards=16 
+        --num_shards=16
     """
 
 
@@ -126,7 +123,7 @@ process deepvariant_combined {
     """
     touch ${samplename}.vcf.gz ${samplename}.vcf.gz.tbi
     touch ${samplename}.gvcf.gz  ${samplename}.gvcf.gz.tbi
-    
+
     """
 
 
@@ -134,20 +131,19 @@ process deepvariant_combined {
 
 process glnexus {
 
- 
     input:
         path(gvcfs)
-    
+
     output:
-        tuple path("germline.v.bcf"), 
+        tuple path("germline.v.bcf"),
         path("germline.norm.vcf.gz"),path("germline.norm.vcf.gz.tbi")
 
-    script: 
+    script:
 
     """
     glnexus_cli --config DeepVariant_unfiltered \
     *.gvcf.gz --threads 8 > germline.v.bcf
-    
+
     bcftools norm \
         -m - \
         -Oz \
@@ -160,18 +156,13 @@ process glnexus {
         -f -t \
         --threads 8 \
         germline.norm.vcf.gz
-    
+
     """
 
     stub:
     """
         touch germline.v.bcf
-        touch germline.norm.vcf.gz 
+        touch germline.norm.vcf.gz
         touch germline.norm.vcf.gz.tbi
     """
 }
-
-
-
-
-
diff --git a/modules/local/qc.nf b/modules/local/qc.nf
index 82bcc1a..f8bbc89 100644
--- a/modules/local/qc.nf
+++ b/modules/local/qc.nf
@@ -13,19 +13,21 @@ ANCESTRY_DB=file(params.genomes[params.genome].somalier_ancestrydb)
 SCRIPT_PATH_GENDER = file(params.script_genderPrediction)
 SCRIPT_PATH_SAMPLES = file(params.script_combineSamples)
 SCRIPT_PATH_PCA = file(params.script_ancestry)
-    
 
-//OUTPUT DIRECTORY 
+
+//OUTPUT DIRECTORY
 process fc_lane {
+    container = "${params.containers.logan}"
+
     label 'process_low'
 
     input:
         tuple val(samplename), path(fqs)
 
-    output: 
+    output:
         tuple val(samplename),
-        path("${samplename}.fastq.info.txt")    
-    
+        path("${samplename}.fastq.info.txt")
+
     script:
     GET_FLOWCELL_LANES=file(params.get_flowcell_lanes)
 
@@ -35,7 +37,7 @@ process fc_lane {
     ${samplename} > ${samplename}.fastq.info.txt
     """
 
-    stub: 
+    stub:
     """
     touch ${samplename}.fastq.info.txt
     """
@@ -61,7 +63,7 @@ process fastq_screen {
         path("${samplename}.R2.trimmed_screen.png"),
         path("${samplename}.R2.trimmed_screen.txt")
 
-    script: 
+    script:
         FASTQ_SCREEN_CONF=file(params.fastq_screen_conf)
 
         """
@@ -75,7 +77,7 @@ process fastq_screen {
 
         """
 
-    stub: 
+    stub:
     """
     touch ${samplename}.R1.trimmed_screen.html ${samplename}.R1.trimmed_screen.png
     touch ${samplename}.R1.trimmed_screen.txt ${samplename}.R2.trimmed_screen.html
@@ -92,11 +94,11 @@ process kraken {
     @Input:
         Trimmed FastQ files (scatter)
     @Output:
-        Kraken logfile and interative krona report
+        Kraken logfile and interactive krona report
     */
-    
+
     input:
-        tuple val(samplename), 
+        tuple val(samplename),
         path(fqs)
 
     output:
@@ -104,19 +106,19 @@ process kraken {
         //path("${samplename}.trimmed.kraken_bacteria.out.txt"),
         path("${samplename}.trimmed.kraken_bacteria.taxa.txt"),
         path("${samplename}.trimmed.kraken_bacteria.krona.html")
-        
 
-    script: 
+
+    script:
     """
     #Setups temporary directory for
-    #intermediate files with built-in 
+    #intermediate files with built-in
     #mechanism for deletion on exit
-    
-    
+
+
     # Copy kraken2 db to local node storage to reduce filesystem strain
     cp -rv $BACDB .
     kdb_base=\$(basename $BACDB)
-    
+
     kraken2 --db $BACDB \
         --threads 16 --report ${samplename}.trimmed.kraken_bacteria.taxa.txt \
         --output - \
@@ -127,7 +129,7 @@ process kraken {
         ktImportTaxonomy - -o ${samplename}.trimmed.kraken_bacteria.krona.html
     """
 
-    stub: 
+    stub:
     """
     touch  ${samplename}.trimmed.kraken_bacteria.taxa.txt ${samplename}.trimmed.kraken_bacteria.krona.html
     """
@@ -155,18 +157,18 @@ process fastqc {
     //threads: 8
     //module=['fastqc/0.11.9']
 
-    script: 
+    script:
     """
     mkdir -p fastqc
     fastqc -t 8 \
         -f bam \
         -o fastqc \
-        ${samplename}.bqsr.bam 
+        ${samplename}.bqsr.bam
     mv fastqc/${samplename}.bqsr_fastqc.html ${samplename}_fastqc.html
     mv fastqc/${samplename}.bqsr_fastqc.zip ${samplename}_fastqc.zip
     """
 
-    stub: 
+    stub:
     """
     touch  ${samplename}_fastqc.html ${samplename}_fastqc.zip
     """
@@ -174,7 +176,7 @@ process fastqc {
 
 process qualimap_bamqc {
     /*
-    Quality-control step to assess various post-alignment metrics 
+    Quality-control step to assess various post-alignment metrics
     and a secondary method to calculate insert size. Please see
     QualiMap's website for more information about BAM QC:
     http://qualimap.conesalab.org/
@@ -182,15 +184,15 @@ process qualimap_bamqc {
         Recalibrated BAM file (scatter)
     @Output:
         Report containing post-aligment quality-control metrics
-    */    
+    */
 
     input:
         tuple val(samplename), path(bam), path(bai)
 
-    output: 
+    output:
         tuple path("${samplename}_genome_results.txt"), path("${samplename}_qualimapReport.html")
 
-    script: 
+    script:
     """
     unset DISPLAY
     qualimap bamqc -bam ${bam} \
@@ -215,31 +217,31 @@ process qualimap_bamqc {
 
 process samtools_flagstats {
     /*
-    Quality-control step to assess alignment quality. Flagstat provides 
-    counts for each of 13 categories based primarily on bit flags in the 
-    FLAG field. Information on the meaning of the flags is given in the 
+    Quality-control step to assess alignment quality. Flagstat provides
+    counts for each of 13 categories based primarily on bit flags in the
+    FLAG field. Information on the meaning of the flags is given in the
     SAM specification: https://samtools.github.io/hts-specs/SAMv1.pdf
     @Input:
         Recalibrated BAM file (scatter)
     @Output:
         Text file containing alignment statistics
     */
-    label 'process_mid'
-    
+    label 'process_medium'
+
     input:
         tuple val(samplename), path(bam), path(bai)
-    
+
     output:
         path("${samplename}.samtools_flagstat.txt")
 
-    script: 
+    script:
     """
     samtools flagstat ${bam} > ${samplename}.samtools_flagstat.txt
     """
 
     stub:
     """
-    touch ${samplename}.samtools_flagstat.txt    
+    touch ${samplename}.samtools_flagstat.txt
     """
 }
 
@@ -260,7 +262,7 @@ process mosdepth {
     */
     input:
         tuple val(samplename), path(bam), path(bai)
-    
+
     output:
         path("${samplename}.mosdepth.region.dist.txt"),
         path("${samplename}.mosdepth.summary.txt"),
@@ -268,7 +270,7 @@ process mosdepth {
         path("${samplename}.regions.bed.gz.csi")
 
 
-    script: 
+    script:
     """
     mosdepth -n --fast-mode --by 500  ${samplename} ${bam} -t $task.cpus
     """
@@ -282,28 +284,28 @@ process mosdepth {
     """
 }
 
-process vcftools {    
+process vcftools {
     /*
-    Quality-control step to calculates a measure of heterozygosity on 
+    Quality-control step to calculates a measure of heterozygosity on
     a per-individual basis. The inbreeding coefficient, F, is estimated
     for each individual using a method of moments. Please see VCFtools
-    documentation for more information: 
+    documentation for more information:
     https://vcftools.github.io/man_latest.html
     @Input:
         Multi-sample gVCF file (indirect-gather-due-to-aggregation)
     @Output:
         Text file containing a measure of heterozygosity
     */
-    label 'process_mid'
+    label 'process_medium'
+
 
-    
-    input: 
+    input:
         tuple path(germlinevcf),path(germlinetbi)
-    output: 
+    output:
        path("variants_raw_variants.het")
-    
-    
-    script: 
+
+
+    script:
     """
     vcftools --gzvcf ${germlinevcf} --het --out variants_raw_variants
     """
@@ -323,16 +325,16 @@ process collectvariantcallmetrics {
     @Input:
         Multi-sample gVCF file (indirect-gather-due-to-aggregation)
     @Output:
-        Text file containing a collection of metrics relating to snps and indels 
-    */    
-    input: 
+        Text file containing a collection of metrics relating to snps and indels
+    */
+    input:
         tuple path(germlinevcf),path(germlinetbi)
-    
-    output: 
+
+    output:
         tuple path("raw_variants.variant_calling_detail_metrics"),
         path("raw_variants.variant_calling_summary_metrics")
 
-       
+
     script:
     """
     java -Xmx24g -jar \${PICARDJARPATH}/picard.jar \
@@ -341,7 +343,7 @@ process collectvariantcallmetrics {
         OUTPUT= "raw_variants" \
         DBSNP=$DBSNP Validation_Stringency=SILENT
     """
-    
+
     stub:
     """
     touch raw_variants.variant_calling_detail_metrics raw_variants.variant_calling_summary_metrics
@@ -354,9 +356,9 @@ process bcftools_stats {
     /*
     Quality-control step to collect summary statistics from bcftools stats.
     When bcftools stats is run with one VCF file then stats by non-reference
-    allele frequency, depth distribution, stats by quality and per-sample 
-    counts, singleton statsistics are calculated. Please see bcftools' 
-    documentation for more information: 
+    allele frequency, depth distribution, stats by quality and per-sample
+    counts, singleton statsistics are calculated. Please see bcftools'
+    documentation for more information:
     http://samtools.github.io/bcftools/bcftools.html#stats
     @Input:
         Per sample gVCF file (scatter)
@@ -364,14 +366,14 @@ process bcftools_stats {
         Text file containing a collection of summary statistics
     */
 
-    label 'process_mid'
+    label 'process_medium'
 
     input:
         tuple val(samplename),  path("${samplename}.gvcf.gz"),path("${samplename}.gvcf.gz.tbi")
     output:
         path("${samplename}.germline.bcftools_stats.txt")
-    
-    script: 
+
+    script:
     """
     bcftools stats ${samplename}.gvcf.gz > ${samplename}.germline.bcftools_stats.txt
     """
@@ -385,22 +387,22 @@ process bcftools_stats {
 
 process gatk_varianteval {
     /*
-    Quality-control step to calculate various quality control metrics from a 
-    variant callset. These metrics include the number of raw or filtered SNP 
+    Quality-control step to calculate various quality control metrics from a
+    variant callset. These metrics include the number of raw or filtered SNP
     counts; ratio of transition mutations to transversions; concordance of a
     particular sample's calls to a genotyping chip; number of s per sample.
-    Please see GATK's documentation for more information: 
+    Please see GATK's documentation for more information:
     https://gatk.broadinstitute.org/hc/en-us/articles/360040507171-VariantEval
     @Input:
         Per sample gVCF file (scatter)
     @Output:
         Evaluation table containing a collection of summary statistics
     */
-    label 'process_mid'
+    label 'process_medium'
 
-    input: 
+    input:
         tuple val(samplename), path("${samplename}.gvcf.gz") ,path("${samplename}.gvcf.gz.tbi")
-    output: 
+    output:
         path("${samplename}.germline.eval.grp")
     //params:
      //   rname    = "vareval",
@@ -410,7 +412,7 @@ process gatk_varianteval {
     //message: "Running GATK4 VariantEval on '{input.vcf}' input file"
     //container: config['images']['wes_base']
     //threads: 16
-    script: 
+    script:
     """
     gatk --java-options '-Xmx12g -XX:ParallelGCThreads=16' VariantEval \
         -R $GENOMEREF \
@@ -431,23 +433,23 @@ process snpeff {
     /*
     Data processing and quality-control step to annotate variants, predict its
     functional effects, and collect various summary statistics about variants and
-    their annotations. Please see SnpEff's documentation for more information: 
+    their annotations. Please see SnpEff's documentation for more information:
     https://pcingola.github.io/SnpEff/
     @Input:
         Per sample gVCF file (scatter)
     @Output:
         Evaluation table containing a collection of summary statistics
     */
-    label 'process_mid'
+    label 'process_medium'
 
-    input:  
+    input:
         tuple val(samplename), path("${samplename}.gvcf.gz"), path("${samplename}.gvcf.gz.tbi")
-    output: 
+    output:
         tuple path("${samplename}.germline.snpeff.ann.vcf"),
         path("${samplename}.germline.snpeff.ann.csv"),
         path("${samplename}.germline.snpeff.ann.html")
 
-    script: 
+    script:
     """
         java -Xmx12g -jar \$SNPEFF_JAR \
         -v -canon -c $SNPEFF_CONFIG \
@@ -478,15 +480,15 @@ process somalier_extract {
 
     input:
         tuple val(samplename), path("${samplename}.bam"), path("${samplename}.bai")
-    output: 
+    output:
         path("output/${samplename}.somalier")
     //params:
     //    sites_vcf = config['references']['SOMALIER']['SITES_VCF'],
     //    genomeFasta = config['references']['GENOME'],
     //    rname = 'somalier_extract'
     //container: config['images']['wes_base']
-    script: 
-    """ 
+    script:
+    """
     mkdir -p output
     somalier extract \
         -d output \
@@ -498,7 +500,7 @@ process somalier_extract {
     stub:
     """
     mkdir -p output
-    touch output/${samplename}.somalier 
+    touch output/${samplename}.somalier
     """
 }
 
@@ -518,21 +520,21 @@ process somalier_analysis_human {
 
     input:
         path(somalierin)
-    
+
     output:
         tuple path("relatedness.pairs.tsv"), path("relatedness.samples.tsv"),
         path("ancestry.somalier-ancestry.tsv"), path("predicted.genders.tsv"),
         path("predicted.pairs.tsv"),
         path("sampleAncestryPCAPlot.html"),
         path("predictedPairsAncestry.pdf")
-    
+
     script:
-    """ 
+    """
     echo "Estimating relatedness"
     somalier relate \
         -o "relatedness" \
         $somalierin
-    
+
     echo "Estimating ancestry"
     somalier ancestry \
         -o "ancestry" \
@@ -542,19 +544,19 @@ process somalier_analysis_human {
 
     Rscript $SCRIPT_PATH_GENDER \
         relatedness.samples.tsv \
-        predicted.genders.tsv    
-    
+        predicted.genders.tsv
+
     Rscript $SCRIPT_PATH_SAMPLES \
         relatedness.pairs.tsv \
         predicted.pairs.tsv
-    
+
     Rscript $SCRIPT_PATH_PCA \
         ancestry.somalier-ancestry.tsv \
         predicted.pairs.tsv \
         sampleAncestryPCAPlot.html \
         predictedPairsAncestry.pdf
     """
-    
+
     stub:
 
     """
@@ -581,30 +583,30 @@ process somalier_analysis_mouse {
 
     input:
         path(somalierin)
-    
+
     output:
-        tuple path("relatedness.pairs.tsv"), 
+        tuple path("relatedness.pairs.tsv"),
         path("relatedness.samples.tsv"),
         path("predicted.genders.tsv"),
         path("predicted.pairs.tsv")
-    
+
     script:
-    """ 
+    """
     echo "Estimating relatedness"
     somalier relate \
         -o "relatedness" \
         $somalierin
-    
+
     Rscript $SCRIPT_PATH_GENDER \
         relatedness.samples.tsv \
-        predicted.genders.tsv    
-    
+        predicted.genders.tsv
+
     Rscript $SCRIPT_PATH_SAMPLES \
         relatedness.pairs.tsv \
         predicted.pairs.tsv
-    
+
     """
-    
+
     stub:
 
     """
@@ -612,7 +614,7 @@ process somalier_analysis_mouse {
     touch relatedness.samples.tsv
     touch predicted.genders.tsv
     touch predicted.pairs.tsv
-    
+
     """
 }
 
@@ -620,23 +622,23 @@ process multiqc {
 
     """
     Reporting step to aggregate sample summary statistics and quality-control
-    information across all samples. This will be one of the last steps of the 
-    pipeline. The inputs listed here are to ensure that this step runs last. 
-    During runtime, MultiQC will recurively crawl through the working directory
+    information across all samples. This will be one of the last steps of the
+    pipeline. The inputs listed here are to ensure that this step runs last.
+    During runtime, MultiQC will recursively crawl through the working directory
     and parse files that it supports.
     @Input:
         List of files to ensure this step runs last (gather)
     @Output:
         Interactive MulitQC report and a QC metadata table
     """
-    
-    input:  
+
+    input:
         path(allqcin)
 
-    output: 
+    output:
         path("MultiQC_Report.html")
 
-    script: 
+    script:
 
     """
     multiqc . \
diff --git a/modules/local/structural_variant.nf b/modules/local/structural_variant.nf
index a6f58f4..dda67c7 100644
--- a/modules/local/structural_variant.nf
+++ b/modules/local/structural_variant.nf
@@ -1,7 +1,7 @@
 GENOMEREF=file(params.genomes[params.genome].genome)
 GENOME=params.genome
 BWAGENOME=file(params.genomes[params.genome].bwagenome)
-DBSNP_INDEL=file(params.genomes[params.genome].KNOWNINDELS) 
+DBSNP_INDEL=file(params.genomes[params.genome].KNOWNINDELS)
 
 
 
@@ -10,7 +10,7 @@ process svaba_somatic {
 
     input:
         tuple val(tumorname), path(tumor), path(tumorbai), val(normalname), path(normal), path(normalbai)
-    
+
     output:
         tuple val(tumorname),
         path("${tumor.simpleName}.bps.txt.gz"),
@@ -34,7 +34,7 @@ process svaba_somatic {
     """
 
     stub:
-    
+
     """
     touch "${tumor.simpleName}.bps.txt.gz"
     touch "${tumor.simpleName}.contigs.bam"
@@ -61,7 +61,7 @@ process manta_somatic {
 
     input:
         tuple val(tumorname), path(tumor), path(tumorbai),val(normalname), path(normal), path(normalbai)
-    
+
     output:
         tuple val(tumorname),
         path("${tumor.simpleName}.diplodSV.vcf.gz"),
@@ -80,7 +80,7 @@ process manta_somatic {
         --runDir=wd
 
     wd/runWorkflow.py -m local -j 10 -g 10
-    
+
     mv wd/results/variants/diploidSV.vcf.gz ${tumor.simpleName}.diplodSV.vcf.gz
     mv wd/results/variants/somaticSV.vcf.gz ${tumor.simpleName}.somaticSV.vcf.gz
     mv wd/results/variants/candidateSV.vcf.gz ${tumor.simpleName}.candidateSV.vcf.gz
@@ -89,7 +89,7 @@ process manta_somatic {
     """
 
     stub:
-    
+
     """
     touch ${tumor.simpleName}.diplodSV.vcf.gz
     touch ${tumor.simpleName}.somaticSV.vcf.gz
@@ -140,7 +140,7 @@ process manta_tonly {
 
     input:
         tuple val(tumorname), path(tumor), path(tumorbai)
-    
+
     output:
         tuple val(tumorname),
         path("${tumor.simpleName}.candidateSV.vcf.gz"),
@@ -158,7 +158,7 @@ process manta_tonly {
         --runDir=wd
 
     wd/runWorkflow.py -m local -j 10 -g 10
-    
+
     mv wd/results/variants/candidateSV.vcf.gz ${tumor.simpleName}.candidateSV.vcf.gz
     mv wd/results/variants/candidateSmallIndels.vcf.gz ${tumor.simpleName}.candidateSmallIndels.vcf.gz
     mv wd/results/variants/tumorSV.vcf.gz ${tumor.simpleName}.tumorSV.vcf.gz
@@ -166,7 +166,7 @@ process manta_tonly {
     """
 
     stub:
-    
+
     """
     touch ${tumor.simpleName}.candidateSV.vcf.gz
     touch ${tumor.simpleName}.candidateSmallIndels.vcf.gz
@@ -182,7 +182,7 @@ process svaba_tonly {
 
     input:
         tuple val(tumorname), path(tumor), path(tumorbai)
-    
+
     output:
         tuple val(tumorname),
         path("${tumor.simpleName}.bps.txt.gz"),
@@ -202,7 +202,7 @@ process svaba_tonly {
     """
 
     stub:
-    
+
     """
     touch "${tumor.simpleName}.bps.txt.gz"
     touch "${tumor.simpleName}.contigs.bam"
@@ -221,11 +221,11 @@ process svaba_tonly {
 process gunzip {
 
     input:
-        tuple val(tumorname), 
+        tuple val(tumorname),
         path(vcf), val(sv)
 
     output:
-        tuple val(tumorname), 
+        tuple val(tumorname),
         path("${tumorname}.tumorSV.vcf"), val(sv)
 
     script:
@@ -246,7 +246,7 @@ process survivor_sv {
     module = ['survivor']
 
     input:
-        tuple val(tumorname), 
+        tuple val(tumorname),
         path(vcfs),val(svs)
 
     output:
@@ -275,9 +275,7 @@ process survivor_sv {
 process annotsv_tonly {
      //AnnotSV for Manta/Svaba works with either vcf.gz or .vcf files
      //Requires bedtools,bcftools
-
     module = ['annotsv/3.3.1']
-    publishDir(path: "${outdir}/SV/annotated_tonly", mode: 'copy') 
 
     input:
         tuple val(tumorname), path(somaticvcf), val(sv)
@@ -306,4 +304,4 @@ process annotsv_tonly {
     touch "${sv}/${tumorname}.tsv"
     touch "${sv}/${tumorname}.unannotated.tsv"
     """
-}
\ No newline at end of file
+}
diff --git a/modules/local/trim_align.nf b/modules/local/trim_align.nf
index 4fa34db..1ceb063 100644
--- a/modules/local/trim_align.nf
+++ b/modules/local/trim_align.nf
@@ -3,12 +3,13 @@ KNOWNRECAL = params.genomes[params.genome].KNOWNRECAL
 
 
 process fastp {
-    label 'process_mid'
+    container = "${params.containers.logan}"
+    label 'process_medium'
     tag { name }
 
     input:
     tuple val(samplename), path(fqs)
-    
+
     output:
     tuple val(samplename),
     path("${samplename}.R1.trimmed.fastq.gz"),
@@ -40,15 +41,16 @@ process fastp {
 
 
 process bwamem2 {
+    container = "${params.containers.logan}"
     tag { name }
-    
+
     input:
-        tuple val(samplename), 
+        tuple val(samplename),
         path("${samplename}.R1.trimmed.fastq.gz"),
         path("${samplename}.R2.trimmed.fastq.gz"),
         path("${samplename}.fastp.json"),
         path("${samplename}.fastp.html")
-        
+
     output:
         tuple val(samplename), path("${samplename}.bam"), path("${samplename}.bai")
 
@@ -77,9 +79,9 @@ process bwamem2 {
 
 process bqsr {
     /*
-    Base quality recalibration for all samples 
-    */    
-
+    Base quality recalibration for all samples
+    */
+    container = "${params.containers.logan}"
     label 'process_low'
     input:
         tuple val(samplename), path("${samplename}.bam"), path("${samplename}.bai"), path(bed)
@@ -99,19 +101,20 @@ process bqsr {
 
     stub:
     """
-    touch ${samplename}_${bed.simpleName}.recal_data.grp 
+    touch ${samplename}_${bed.simpleName}.recal_data.grp
     """
 
 }
 
 process gatherbqsr {
+    container = "${params.containers.logan}"
     label 'process_low'
-    input: 
+    input:
         tuple val(samplename), path(recalgroups)
     output:
         tuple val(samplename), path("${samplename}.recal_data.grp")
     script:
-    
+
     strin = recalgroups.join(" --input ")
 
     """
@@ -131,10 +134,11 @@ process gatherbqsr {
 
 process applybqsr {
     /*
-    Base quality recalibration for all samples to 
-    */   
+    Base quality recalibration for all samples to
+    */
+    container = "${params.containers.logan}"
     label 'process_low'
-    
+
     input:
         tuple val(samplename), path("${samplename}.bam"), path("${samplename}.bai"), path("${samplename}.recal_data.grp")
 
@@ -154,7 +158,7 @@ process applybqsr {
     """
 
     stub:
-    
+
     """
     touch ${samplename}.bqsr.bam ${samplename}.bqsr.bai
     """
@@ -164,12 +168,12 @@ process applybqsr {
 
 
 process samtoolsindex {
-    label 'process_mid'
-    publishDir(path: "${outdir}/bams/BQSR", mode: 'copy') 
-    
+    container = "${params.containers.logan}"
+    label 'process_medium'
+
     input:
     tuple val(bamname), path(bam)
-    
+
     output:
     tuple val(bamname), path(bam), path("${bam}.bai")
 
@@ -187,9 +191,10 @@ process samtoolsindex {
 
 //Save to CRAM for output
 process bamtocram_tonly {
-    label 'process_mid'
-    
-    input: 
+    container = "${params.containers.logan}"
+    label 'process_medium'
+
+    input:
         tuple val(tumorname), path(tumor), path(tumorbai)
 
     output:
@@ -204,27 +209,27 @@ process bamtocram_tonly {
 
 /*
 process indelrealign {
-    //Briefly, RealignerTargetCreator runs faster with increasing -nt threads, 
+    //Briefly, RealignerTargetCreator runs faster with increasing -nt threads,
     //while IndelRealigner shows diminishing returns for increasing scatter
-    
+
     tag { name }
-    
+
     input:
     tuple val(samplename), path("${samplename}.bam"), path("${samplename}.bai")
 
     output:
     tuple val(samplename), path("${samplename}.ir.bam")
 
-    script: 
-    
+    script:
+
     """
     /usr/bin/java -Xmx32g -jar \${GATK_JAR} -T RealignerTargetCreator \
         -I ${samplename}.bam \
         -R ${GENOMEREF} \
         -o ${samplename}.intervals \
         -nt 16 \
-        -known ${MILLSINDEL} -known ${SHAPEITINDEL} 
-    
+        -known ${MILLSINDEL} -known ${SHAPEITINDEL}
+
     /usr/bin/java -Xmx32g -jar \${GATK_JAR} -T IndelRealigner \
         -R ${GENOMEREF} \
         -I ${samplename}.bam \
@@ -234,11 +239,11 @@ process indelrealign {
         -targetIntervals ${samplename}.intervals \
         -o  ${samplename}.ir.bam
     """
-    
+
 
     stub:
     """
-    touch ${samplename}.ir.bam 
+    touch ${samplename}.ir.bam
     """
 
 }
diff --git a/modules/local/variant_calling.nf b/modules/local/variant_calling.nf
index e23cd0e..ef25413 100644
--- a/modules/local/variant_calling.nf
+++ b/modules/local/variant_calling.nf
@@ -1,10 +1,10 @@
 GENOMEREF=file(params.genomes[params.genome].genome)
 GENOMEFAI=file(params.genomes[params.genome].genomefai)
 GENOMEDICT=file(params.genomes[params.genome].genomedict)
-KGPGERMLINE=params.genomes[params.genome].kgp 
-DBSNP=file(params.genomes[params.genome].dbsnp) 
-GNOMADGERMLINE=params.genomes[params.genome].gnomad 
-PON=file(params.genomes[params.genome].pon) 
+KGPGERMLINE=params.genomes[params.genome].kgp
+DBSNP=file(params.genomes[params.genome].dbsnp)
+GNOMADGERMLINE=params.genomes[params.genome].gnomad
+PON=file(params.genomes[params.genome].pon)
 VEPCACHEDIR=file(params.genomes[params.genome].vepcache)
 VEPSPECIES=params.genomes[params.genome].vepspecies
 VEPBUILD=params.genomes[params.genome].vepbuild
@@ -15,20 +15,21 @@ LOFREQ_CONVERT=params.lofreq_convert
 
 
 process mutect2 {
+    container "${params.containers.logan}"
     label 'process_somaticcaller'
 
     input:
         tuple val(tumorname), path(tumor), path(tumorbai),
-        val(normalname), path(normal), path(normalbai), 
+        val(normalname), path(normal), path(normalbai),
         path(bed)
-    
+
     output:
         tuple val(tumorname), val(normalname),
         path("${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.mut2.vcf.gz"),
         path("${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.f1r2.tar.gz"),
         path("${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.mut2.vcf.gz.stats")
 
-    
+
     script:
     """
     gatk Mutect2 \
@@ -55,12 +56,13 @@ process mutect2 {
 
 
 process pileup_paired_t {
+    container "${params.containers.logan}"
     label 'process_highmem'
 
     input:
         tuple val(tumorname), path(tumor), path(tumorbai),
         val(normalname), path(normal), path(normalbai), path(bed)
-    
+
     output:
         tuple val(tumorname),
         path("${tumor.simpleName}_${bed.simpleName}.tumor.pileup.table")
@@ -71,7 +73,7 @@ process pileup_paired_t {
         -I ${tumor} \
         -V $KGPGERMLINE \
         -L ${bed} \
-        -O ${tumor.simpleName}_${bed.simpleName}.tumor.pileup.table 
+        -O ${tumor.simpleName}_${bed.simpleName}.tumor.pileup.table
 
     """
 
@@ -84,12 +86,13 @@ process pileup_paired_t {
 
 
 process pileup_paired_n {
+    container "${params.containers.logan}"
     label 'process_highmem'
 
     input:
         tuple val(tumorname), path(tumor), path(tumorbai),
         val(normalname), path(normal), path(normalbai), path(bed)
-    
+
     output:
         tuple val(tumorname),
         path("${tumor.simpleName}_${bed.simpleName}.normal.pileup.table")
@@ -100,10 +103,10 @@ process pileup_paired_n {
         -I ${normal} \
         -V $KGPGERMLINE \
         -L ${bed} \
-        -O ${tumor.simpleName}_${bed.simpleName}.normal.pileup.table 
+        -O ${tumor.simpleName}_${bed.simpleName}.normal.pileup.table
 
     """
-    
+
     stub:
     """
     touch ${tumor.simpleName}_${bed.simpleName}.normal.pileup.table
@@ -113,13 +116,14 @@ process pileup_paired_n {
 
 
 process contamination_paired {
+    container "${params.containers.logan}"
     label 'process_highmem'
 
     input:
         tuple val(tumorname),
         path(tumor_pileups),
         path(normal_pileups)
-    
+
     output:
         tuple val(tumorname),
         path("${tumorname}_allpileups.table"),
@@ -137,7 +141,7 @@ process contamination_paired {
     gatk GatherPileupSummaries \
     --sequence-dictionary $GENOMEDICT \
     -I ${alltumor} -O ${tumorname}_allpileups.table
-    
+
     gatk GatherPileupSummaries \
     --sequence-dictionary $GENOMEDICT \
     -I ${allnormal} -O ${tumorname}_normal.allpileups.table
@@ -161,20 +165,21 @@ process contamination_paired {
     touch ${tumorname}_normal.contamination.table
     """
 
-    
+
 }
 
 
 process learnreadorientationmodel {
+    container "${params.containers.logan}"
     label 'process_highmem'
 
     input:
         tuple val(sample), path(f1r2)
-      
+
     output:
         tuple val(sample), path("${sample}.read-orientation-model.tar.gz")
 
-    script: 
+    script:
     f1r2in = f1r2.join(" --input ")
 
     """
@@ -191,15 +196,16 @@ process learnreadorientationmodel {
 
 
 process mergemut2stats {
+    container "${params.containers.logan}"
     label 'process_low'
 
     input:
         tuple val(sample), path(stats)
-      
+
     output:
         tuple val(sample), path("${sample}.final.stats")
 
-    script: 
+    script:
     statsin = stats.join(" --stats ")
 
     """
@@ -217,17 +223,18 @@ process mergemut2stats {
 
 
 process mutect2filter {
-    label 'process_mid'
-        
+    container "${params.containers.logan}"
+    label 'process_medium'
+
     input:
-        tuple val(tumor), val(normal),path(mutvcfs), path(stats), path(obs), 
+        tuple val(tumor), val(normal),path(mutvcfs), path(stats), path(obs),
         path(pileups), path(normal_pileups),path(tumorcontamination),path(normalcontamination)
-    
+
     output:
-        tuple val("${tumor}_vs_${normal}"), 
-        path("${tumor}_vs_${normal}.mut2.marked.vcf.gz"), 
+        tuple val("${tumor}_vs_${normal}"),
+        path("${tumor}_vs_${normal}.mut2.marked.vcf.gz"),
         path("${tumor}_vs_${normal}.mut2.marked.vcf.gz.tbi"),
-        path("${tumor}_vs_${normal}.mut2.norm.vcf.gz"), path("${tumor}_vs_${normal}.mut2.norm.vcf.gz.tbi"), 
+        path("${tumor}_vs_${normal}.mut2.norm.vcf.gz"), path("${tumor}_vs_${normal}.mut2.norm.vcf.gz.tbi"),
         path("${tumor}_vs_${normal}.mut2.marked.vcf.gz.filteringStats.tsv")
 
     script:
@@ -247,7 +254,7 @@ process mutect2filter {
         --variant ${tumor}_vs_${normal}.mut2.marked.vcf.gz \
         --exclude-filtered \
         --output ${tumor}_vs_${normal}.mut2.final.vcf.gz
-    
+
     bcftools sort ${tumor}_vs_${normal}.mut2.final.vcf.gz |\
     bcftools norm --threads $task.cpus --check-ref s -f $GENOMEREF -O v |\
         awk '{{gsub(/\\y[W|K|Y|R|S|M|B|D|H|V]\\y/,"N",\$4); OFS = "\t"; print}}' |\
@@ -267,18 +274,19 @@ process mutect2filter {
 
 
 process strelka_tn {
+    container "${params.containers.logan}"
     label 'process_highcpu'
     input:
-        tuple val(tumorname), path(tumor), path(tumorbai), 
+        tuple val(tumorname), path(tumor), path(tumorbai),
         val(normalname), path(normal), path(normalbai), path(bed)
-    
+
     output:
         tuple val(tumorname), val(normalname),
         path("${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic.snvs.vcf.gz"),
         path("${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic.snvs.vcf.gz.tbi"),
         path("${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic.indels.vcf.gz"),
         path("${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic.indels.vcf.gz.tbi")
-    
+
     script:
 
     """
@@ -296,21 +304,21 @@ process strelka_tn {
     ./wd/runWorkflow.py -m local -j $task.cpus
     mv wd/results/variants/somatic.snvs.vcf.gz  ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic_temp.snvs.vcf.gz
     mv wd/results/variants/somatic.indels.vcf.gz  ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic_temp.indels.vcf.gz
-    
-    printf "NORMAL\t${normalname}\nTUMOR\t${tumorname}\n" >sampname 
-    
+
+    printf "NORMAL\t${normalname}\nTUMOR\t${tumorname}\n" >sampname
+
     bcftools reheader -s sampname ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic_temp.snvs.vcf.gz \
-        | bcftools view -Oz -o ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic.snvs.vcf.gz 
+        | bcftools view -Oz -o ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic.snvs.vcf.gz
     bcftools reheader -s sampname ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic_temp.indels.vcf.gz \
-        | bcftools view -Oz -o ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic.indels.vcf.gz 
+        | bcftools view -Oz -o ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic.indels.vcf.gz
 
     bcftools index -t ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic.snvs.vcf.gz
-    bcftools index -t ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic.indels.vcf.gz 
-  
+    bcftools index -t ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic.indels.vcf.gz
+
     """
 
     stub:
-    
+
     """
     touch ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic.snvs.vcf.gz  ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic.snvs.vcf.gz.tbi
     touch ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic.indels.vcf.gz ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.somatic.indels.vcf.gz.tbi
@@ -321,16 +329,17 @@ process strelka_tn {
 
 
 process vardict_tn {
-    label 'process_highcpu'
+    container "${params.containers.logan}"
+    label 'process_somaticcaller_high'
 
     input:
         tuple val(tumorname), path(tumor), path(tumorbai), val(normalname), path(normal), path(normalbai), path(bed)
-    
+
     output:
         tuple val(tumorname), val(normalname),
         path("${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.vardict.vcf.gz")
-    //bcbio notes of vardict filtering var2vcf_paired.pl -P 0.9 -m 4.25 -f 0.01 -M” and 
-    //filtered with “((AF*DP < 6) && ((MQ < 55.0 && NM > 1.0) || (MQ < 60.0 && NM > 2.0) || (DP < 10) || (QUAL < 45)))” 
+    //bcbio notes of vardict filtering var2vcf_paired.pl -P 0.9 -m 4.25 -f 0.01 -M” and
+    //filtered with “((AF*DP < 6) && ((MQ < 55.0 && NM > 1.0) || (MQ < 60.0 && NM > 2.0) || (DP < 10) || (QUAL < 45)))”
     script:
 
     """
@@ -350,8 +359,8 @@ process vardict_tn {
             -S \
             -f 0.05 >  ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.vardict.vcf
 
-    printf "${normal.Name}\t${normalname}\n${tumor.Name}\t${tumorname}\n" > sampname 
-    
+    printf "${normal.Name}\t${normalname}\n${tumor.Name}\t${tumorname}\n" > sampname
+
     bcftools reheader -s sampname ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.vardict.vcf \
         | bcftools view -Oz -o ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.vardict.vcf.gz
 
@@ -359,7 +368,7 @@ process vardict_tn {
     """
 
     stub:
-    
+
     """
     touch ${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.vardict.vcf.gz
 
@@ -370,19 +379,20 @@ process vardict_tn {
 
 
 process varscan_tn {
+    container "${params.containers.logan}"
     label 'process_somaticcaller'
 
     input:
-        tuple val(tumorname), path(tumor), path(tumorbai), 
+        tuple val(tumorname), path(tumor), path(tumorbai),
         val(normalname), path(normal), path(normalbai), path(bed),
         val(tumor1),
-        path(tumorpileup), path(normalpileup), 
+        path(tumorpileup), path(normalpileup),
         path(tumor_con_table), path(normal_con_table)
-    
+
     output:
         tuple val(tumorname), val(normalname),
         path("${tumor.simpleName}_vs_${normal.simpleName}_${bed.simpleName}.varscan.vcf.gz")
-    
+
     shell:
     '''
     tumor_purity=$( echo "1-$(printf '%.6f' $(tail -n -1 !{tumor_con_table} | cut -f2 ))" | bc -l)
@@ -402,8 +412,8 @@ process varscan_tn {
     -R !{GENOMEREF} -SD !{GENOMEDICT} \
     -O !{tumor.simpleName}_vs_!{normal.simpleName}_!{bed.simpleName}_temp.varscan.vcf
 
-    printf "NORMAL\t!{normalname}\nTUMOR\t!{tumorname}\n" > sampname 
-    
+    printf "NORMAL\t!{normalname}\nTUMOR\t!{tumorname}\n" > sampname
+
     bcftools reheader -s sampname !{tumor.simpleName}_vs_!{normal.simpleName}_!{bed.simpleName}_temp.varscan.vcf \
        | bcftools view -Oz -o !{tumor.simpleName}_vs_!{normal.simpleName}_!{bed.simpleName}.varscan.vcf.gz
 
@@ -418,17 +428,18 @@ process varscan_tn {
 
 
 process octopus_tn {
-    //label 'process_highcpu' Using separate docker for octopus
+    container "${params.containers.octopus}"
+    label 'process_somaticcaller_high'
 
     input:
-        tuple val(tumorname), path(tumor), path(tumorbai), 
+        tuple val(tumorname), path(tumor), path(tumorbai),
         val(normalname), path(normal), path(normalbai), path(bed)
-    
+
 
     output:
         tuple val("${tumorname}_vs_${normalname}"),
         path("${tumorname}_vs_${normalname}_${bed.simpleName}.octopus.vcf.gz")
-    
+
     script:
 
     """
@@ -443,32 +454,33 @@ process octopus_tn {
     """
 
     stub:
-    
+
     """
     touch "${tumorname}_vs_${normalname}_${bed.simpleName}.octopus.vcf.gz"
     """
 
-} 
+}
 
 
 process lofreq_tn {
-    label 'process_somaticcaller' 
+    container "${params.containers.logan}"
+    label 'process_somaticcaller'
 
     input:
-        tuple val(tumorname), path(tumor), path(tumorbai), 
+        tuple val(tumorname), path(tumor), path(tumorbai),
         val(normalname), path(normal), path(normalbai), path(bed)
-    
+
 
     output:
-    
-        tuple val(tumorname), val(normalname), 
+
+        tuple val(tumorname), val(normalname),
         path("${tumorname}_vs_${normalname}_${bed.simpleName}_somatic_final.snvs.vcf.gz"),
         path("${tumorname}_vs_${normalname}_${bed.simpleName}_somatic_final_minus-dbsnp.snvs.vcf.gz"),
         path("${tumorname}_vs_${normalname}_${bed.simpleName}_somatic_final.indels.vcf.gz"),
         path("${tumorname}_vs_${normalname}_${bed.simpleName}_somatic_final_minus-dbsnp.indels.vcf.gz"),
         path("${tumorname}_vs_${normalname}_${bed.simpleName}_lofreq.vcf.gz"),
         path("${tumorname}_vs_${normalname}_${bed.simpleName}_lofreq.vcf.gz.tbi")
-    
+
     script:
 
     """
@@ -478,16 +490,16 @@ process lofreq_tn {
         -l ${bed} \
         --call-indels \
         -o ${tumorname}_vs_${normalname}_${bed.simpleName}_
-    
+
     bcftools concat ${tumorname}_vs_${normalname}_${bed.simpleName}_somatic_final_minus-dbsnp.snvs.vcf.gz \
         ${tumorname}_vs_${normalname}_${bed.simpleName}_somatic_final_minus-dbsnp.indels.vcf.gz --threads $task.cpus -Oz -o \
         ${tumorname}_vs_${normalname}_${bed.simpleName}_temp_lofreq.vcf.gz
 
     $LOFREQ_CONVERT -i ${tumorname}_vs_${normalname}_${bed.simpleName}_temp_lofreq.vcf.gz -g 1/0 \
         -n ${tumorname} -o ${tumorname}_vs_${normalname}_${bed.simpleName}_temp1_lofreq.vcf.gz
-    
+
     bcftools view -h ${tumorname}_vs_${normalname}_${bed.simpleName}_temp1_lofreq.vcf.gz >temphead
-    
+
     sed 's/^##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">/##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref\\/fwd, ref\\/rev, var\\/fwd, var\\/rev">/' temphead > temphead1
     bcftools reheader ${tumorname}_vs_${normalname}_${bed.simpleName}_temp1_lofreq.vcf.gz -h temphead1 |\
         bcftools view -Oz -o ${tumorname}_vs_${normalname}_${bed.simpleName}_lofreq.vcf.gz
@@ -497,71 +509,73 @@ process lofreq_tn {
     """
 
     stub:
-    
+
     """
     touch "${tumorname}_vs_${normalname}_${bed.simpleName}_somatic_final.snvs.vcf.gz"
     touch "${tumorname}_vs_${normalname}_${bed.simpleName}_somatic_final_minus-dbsnp.snvs.vcf.gz"
     touch "${tumorname}_vs_${normalname}_${bed.simpleName}_somatic_final.indels.vcf.gz"
     touch "${tumorname}_vs_${normalname}_${bed.simpleName}_somatic_final_minus-dbsnp.indels.vcf.gz"
     touch "${tumorname}_vs_${normalname}_${bed.simpleName}_lofreq.vcf.gz" "${tumorname}_vs_${normalname}_${bed.simpleName}_lofreq.vcf.gz.tbi"
-    
+
     """
-} 
+}
 
 
 
 process muse_tn {
-    label 'process_somaticcaller' 
+    container "${params.containers.logan}"
+    label 'process_somaticcaller'
     input:
-        tuple val(tumorname), path(tumor), path(tumorbai), 
+        tuple val(tumorname), path(tumor), path(tumorbai),
         val(normalname), path(normal), path(normalbai)
-    
+
 
     output:
         tuple val(tumorname), val(normalname),
         path("${tumorname}_vs_${normalname}.vcf.gz")
-    
+
     script:
 
     """
     MuSE call -f $GENOMEREF -O ${tumorname}_vs_${normalname} -n $task.cpus $tumor $normal
     MuSE sump -I ${tumorname}_vs_${normalname}.MuSE.txt \
         -O ${tumorname}_vs_${normalname}.vcf -n $task.cpus -D $DBSNP -G
-    
+
     bcftools view ${tumorname}_vs_${normalname}.vcf -Oz -o ${tumorname}_vs_${normalname}_temp.vcf.gz
 
-    printf "NORMAL\t${normalname}\nTUMOR\t${tumorname}\n" > sampname 
-    
+    printf "NORMAL\t${normalname}\nTUMOR\t${tumorname}\n" > sampname
+
     bcftools reheader -s sampname ${tumorname}_vs_${normalname}_temp.vcf.gz \
         | bcftools view -Oz -o ${tumorname}_vs_${normalname}.vcf.gz
 
     """
 
     stub:
-    
+
     """
     touch "${tumorname}_vs_${normalname}.vcf.gz"
     """
 
-} 
+}
 
 
 process combineVariants {
+    container "${params.containers.logan}"
     label 'process_highmem'
 
     input:
         tuple val(sample), path(inputvcf), val(vc)
-    
+
     output:
-        tuple val(sample), 
-        path("${vc}/${sample}.${vc}.marked.vcf.gz"), 
-        path("${vc}/${sample}.${vc}.marked.vcf.gz.tbi"), 
+        tuple val(sample),
+        path("${vc}/${sample}.${vc}.marked.vcf.gz"),
+        path("${vc}/${sample}.${vc}.marked.vcf.gz.tbi"),
         path("${vc}/${sample}.${vc}.norm.vcf.gz"),
         path("${vc}/${sample}.${vc}.norm.vcf.gz.tbi")
 
     script:
     vcfin = inputvcf.join(" -I ")
-    
+
     """
     mkdir ${vc}
     gatk --java-options "-Xmx48g" SortVcf \
@@ -596,21 +610,22 @@ process combineVariants {
 
 
 process combineVariants_alternative {
+    container "${params.containers.logan}"
     label 'process_highmem'
 
     input:
         tuple val(sample), path(vcfs), path(vcfsindex), val(vc)
-    
+
     output:
-        tuple val(sample), 
-        path("${vc}/${sample}.${vc}.marked.vcf.gz"), 
-        path("${vc}/${sample}.${vc}.marked.vcf.gz.tbi"), 
+        tuple val(sample),
+        path("${vc}/${sample}.${vc}.marked.vcf.gz"),
+        path("${vc}/${sample}.${vc}.marked.vcf.gz.tbi"),
         path("${vc}/${sample}.${vc}.norm.vcf.gz"),
         path("${vc}/${sample}.${vc}.norm.vcf.gz.tbi")
-    
+
     script:
     vcfin = vcfs.join(" ")
-    
+
     """
     mkdir ${vc}
     bcftools concat $vcfin -a -Oz -o ${sample}.${vc}.temp1.vcf.gz
@@ -636,13 +651,14 @@ process combineVariants_alternative {
     touch ${vc}/${sample}.${vc}.norm.vcf.gz
     touch ${vc}/${sample}.${vc}.marked.vcf.gz.tbi
     touch ${vc}/${sample}.${vc}.norm.vcf.gz.tbi
-    
+
     """
 
 }
 
 
 process bcftools_index_octopus {
+    container "${params.containers.logan}"
     label 'process_low'
 
     input:
@@ -651,10 +667,10 @@ process bcftools_index_octopus {
 
     output:
         tuple val(tumor),
-        path(vcf), 
+        path(vcf),
         path("${vcf}.tbi")
-    
-    script:    
+
+    script:
     """
     bcftools index -t ${vcf}
     """
@@ -670,32 +686,33 @@ process bcftools_index_octopus {
 
 process combineVariants_strelka {
     //Concat all somatic snvs/indels across all files, strelka separates snv/indels
-    label 'process_mid'
+    container "${params.containers.logan}"
+    label 'process_medium'
 
     input:
-        tuple val(sample), 
+        tuple val(sample),
         path(strelkasnvs), path(snvindex),
         path(strelkaindels), path(indelindex)
-    
+
     output:
-        tuple val(sample), 
+        tuple val(sample),
         path("${sample}.strelka.vcf.gz"), path("${sample}.strelka.vcf.gz.tbi"),
         path("${sample}.filtered.strelka.vcf.gz"), path("${sample}.filtered.strelka.vcf.gz.tbi")
-    
-    
+
+
     script:
-    
+
     vcfin = strelkasnvs.join(" ")
     indelsin = strelkaindels.join(" ")
 
 
     """
-    bcftools concat $vcfin $indelsin --threads $task.cpus -Oz -o ${sample}.temp.strelka.vcf.gz -a 
+    bcftools concat $vcfin $indelsin --threads $task.cpus -Oz -o ${sample}.temp.strelka.vcf.gz -a
     bcftools norm ${sample}.temp.strelka.vcf.gz -m- --threads $task.cpus --check-ref s -f $GENOMEREF -O v |\
         awk '{{gsub(/\\y[W|K|Y|R|S|M|B|D|H|V]\\y/,"N",\$4); OFS = "\t"; print}}' |\
         sed '/^\$/d' > ${sample}.temp1.strelka.vcf.gz
 
-    bcftools sort ${sample}.temp1.strelka.vcf.gz -Oz -o ${sample}.strelka.vcf.gz 
+    bcftools sort ${sample}.temp1.strelka.vcf.gz -Oz -o ${sample}.strelka.vcf.gz
 
     bcftools view ${sample}.strelka.vcf.gz --threads $task.cpus -f PASS -Oz -o ${sample}.filtered.strelka.vcf.gz
 
@@ -708,16 +725,17 @@ process combineVariants_strelka {
     """
     touch ${sample}.strelka.vcf.gz ${sample}.strelka.vcf.gz.tbi
     touch ${sample}.filtered.strelka.vcf.gz ${sample}.filtered.strelka.vcf.gz.tbi
-    
+
     """
 
 }
 
 
 process somaticcombine {
-    label 'process_mid'
+    container "${params.containers.logan}"
+    label 'process_medium'
 
-    input: 
+    input:
         tuple val(tumorsample), val(normal),
         val(callers),
         path(vcfs), path(vcfindex)
@@ -730,7 +748,7 @@ process somaticcombine {
     script:
         vcfin1=[callers, vcfs].transpose().collect { a, b -> a + " " + b }
         vcfin2="-V:" + vcfin1.join(" -V:")
-    
+
     """
     java -jar \$DISCVRSeq_JAR MergeVcfsAndGenotypes \
         -R $GENOMEREF \
@@ -753,10 +771,13 @@ process somaticcombine {
 }
 
 
-process annotvep_tn {    
+process annotvep_tn {
+    label 'process_medium'
+    container "${params.containers.vcf2maf}"
+
     input:
-        tuple val(tumorsample), val(normalsample), 
-        val(vc), path(tumorvcf), path(vcfindex) 
+        tuple val(tumorsample), val(normalsample),
+        val(vc), path(tumorvcf), path(vcfindex)
 
     output:
         path("paired/${vc}/${tumorsample}_vs_${normalsample}.maf")
@@ -771,15 +792,15 @@ process annotvep_tn {
     NORM_VCF_ID_ARG=""
     NSAMPLES=${#VCF_SAMPLE_IDS[@]}
     if [ $NSAMPLES -gt 1 ]; then
-        # Assign tumor, normal IDs 
-        # Look through column names and 
+        # Assign tumor, normal IDs
+        # Look through column names and
         # see if they match provided IDs
         for (( i = 0; i < $NSAMPLES; i++ )); do
             echo "${VCF_SAMPLE_IDS[$i]}"
             if [ "${VCF_SAMPLE_IDS[$i]}" == !{tumorsample} ]; then
                 TID_IDX=$i
             fi
-            
+
             if [ "${VCF_SAMPLE_IDS[$i]}" == !{normalsample} ]; then
                 NID_IDX=$i
             fi
@@ -791,9 +812,9 @@ process annotvep_tn {
         fi
     fi
     VCF_TID=${VCF_SAMPLE_IDS[$TID_IDX]}
-   
+
     zcat !{tumorvcf} > !{tumorvcf.baseName}
-    
+
     mkdir -p paired/!{vc}
 
     vcf2maf.pl \
@@ -817,10 +838,10 @@ process annotvep_tn {
 
 
 process combinemafs_tn {
+    container "${params.containers.logan}"
     label 'process_low'
-    publishDir(path: "${outdir}/mafs/paired", mode: 'copy')
 
-    input: 
+    input:
         path(allmafs)
 
     output:
@@ -840,5 +861,3 @@ process combinemafs_tn {
     touch final_tn.maf
     """
 }
-
-
diff --git a/modules/local/variant_calling_tonly.nf b/modules/local/variant_calling_tonly.nf
index 9f8bf93..c063f2a 100644
--- a/modules/local/variant_calling_tonly.nf
+++ b/modules/local/variant_calling_tonly.nf
@@ -1,10 +1,10 @@
 GENOMEREF=file(params.genomes[params.genome].genome)
 GENOMEFAI=file(params.genomes[params.genome].genomefai)
 GENOMEDICT=file(params.genomes[params.genome].genomedict)
-KGPGERMLINE=params.genomes[params.genome].kgp 
-DBSNP=file(params.genomes[params.genome].dbsnp) 
-GNOMADGERMLINE=params.genomes[params.genome].gnomad 
-PON=file(params.genomes[params.genome].pon) 
+KGPGERMLINE=params.genomes[params.genome].kgp
+DBSNP=file(params.genomes[params.genome].dbsnp)
+GNOMADGERMLINE=params.genomes[params.genome].gnomad
+PON=file(params.genomes[params.genome].pon)
 VEPCACHEDIR=file(params.genomes[params.genome].vepcache)
 VEPSPECIES=params.genomes[params.genome].vepspecies
 VEPBUILD=params.genomes[params.genome].vepbuild
@@ -13,11 +13,13 @@ GERMLINE_FOREST=params.genomes[params.genome].octopus_gforest
 
 
 process pileup_paired_tonly {
+    container "${params.containers.logan}"
+
     label 'process_highmem'
 
     input:
         tuple val(tumorname), path(tumor), path(tumorbai), path(bed)
-    
+
     output:
         tuple val(tumorname),
         path("${tumor.simpleName}_${bed.simpleName}.tumor.pileup.table")
@@ -29,7 +31,7 @@ process pileup_paired_tonly {
         -I ${tumor} \
         -V $KGPGERMLINE \
         -L ${bed} \
-        -O ${tumor.simpleName}_${bed.simpleName}.tumor.pileup.table 
+        -O ${tumor.simpleName}_${bed.simpleName}.tumor.pileup.table
 
     """
 
@@ -43,6 +45,8 @@ process pileup_paired_tonly {
 
 
 process contamination_tumoronly {
+    container "${params.containers.logan}"
+
     label 'process_highmem'
 
     input:
@@ -63,7 +67,7 @@ process contamination_tumoronly {
     gatk GatherPileupSummaries \
     --sequence-dictionary $GENOMEDICT \
     -I ${alltumor} -O ${tumorname}_allpileups.table
-    
+
     gatk CalculateContamination \
         -I ${tumorname}_allpileups.table \
         -O ${tumorname}.contamination.table
@@ -81,15 +85,17 @@ process contamination_tumoronly {
 
 
 process learnreadorientationmodel_tonly {
+    container "${params.containers.logan}"
+
     label 'process_highmem'
 
     input:
         tuple val(sample), path(f1r2)
-      
+
     output:
     tuple val(sample), path("${sample}.read-orientation-model.tar.gz")
 
-    script: 
+    script:
     f1r2in = f1r2.join(" --input ")
 
     """
@@ -109,15 +115,17 @@ process learnreadorientationmodel_tonly {
 
 
 process mergemut2stats_tonly {
+    container "${params.containers.logan}"
+
     label 'process_low'
 
     input:
         tuple val(sample), path(stats)
-      
+
     output:
         tuple val(sample), path("${sample}.final.stats")
 
-    script: 
+    script:
     statsin = stats.join(" --stats ")
 
     """
@@ -136,16 +144,18 @@ process mergemut2stats_tonly {
 
 
 process mutect2_t_tonly {
+    container "${params.containers.logan}"
     label 'process_somaticcaller'
+
     input:
         tuple val(tumorname), path(tumor), path(tumorbai), path(bed)
-    
+
     output:
         tuple val(tumorname),
         path("${tumor.simpleName}_${bed.simpleName}.tonly.mut2.vcf.gz"),
         path("${tumor.simpleName}_${bed.simpleName}.f1r2.tar.gz"),
         path("${tumor.simpleName}_${bed.simpleName}.tonly.mut2.vcf.gz.stats")
-    
+
     script:
 
     """
@@ -158,7 +168,7 @@ process mutect2_t_tonly {
     --panel-of-normals $PON \
     --output ${tumor.simpleName}_${bed.simpleName}.tonly.mut2.vcf.gz \
     --f1r2-tar-gz ${tumor.simpleName}_${bed.simpleName}.f1r2.tar.gz \
-    --independent-mates    
+    --independent-mates
     """
 
     stub:
@@ -174,14 +184,15 @@ process mutect2_t_tonly {
 
 
 process mutect2filter_tonly {
-    label 'process_mid'
+    container "${params.containers.logan}"
+    label 'process_medium'
 
     input:
         tuple val(sample), path(mutvcfs), path(stats), path(obs), path(pileups),path(tumorcontamination)
     output:
-        tuple val(sample), 
-        path("${sample}.tonly.mut2.marked.vcf.gz"),path("${sample}.tonly.mut2.marked.vcf.gz.tbi"), 
-        path("${sample}.tonly.mut2.norm.vcf.gz"),path("${sample}.tonly.mut2.norm.vcf.gz.tbi"), 
+        tuple val(sample),
+        path("${sample}.tonly.mut2.marked.vcf.gz"),path("${sample}.tonly.mut2.marked.vcf.gz.tbi"),
+        path("${sample}.tonly.mut2.norm.vcf.gz"),path("${sample}.tonly.mut2.norm.vcf.gz.tbi"),
         path("${sample}.tonly.mut2.marked.vcf.gz.filteringStats.tsv")
 
     script:
@@ -190,8 +201,8 @@ process mutect2filter_tonly {
 
 
     """
-    gatk GatherVcfs -I ${mut2in} -O ${sample}.tonly.concat.vcf.gz 
-    gatk IndexFeatureFile -I ${sample}.tonly.concat.vcf.gz 
+    gatk GatherVcfs -I ${mut2in} -O ${sample}.tonly.concat.vcf.gz
+    gatk IndexFeatureFile -I ${sample}.tonly.concat.vcf.gz
     gatk FilterMutectCalls \
         -R $GENOMEREF \
         -V ${sample}.tonly.concat.vcf.gz \
@@ -207,7 +218,7 @@ process mutect2filter_tonly {
         --output ${sample}.tonly.mut2.final.vcf.gz
 
     bcftools sort ${sample}.tonly.mut2.final.vcf.gz |\
-    bcftools norm --threads $task.cpus --check-ref s -f $GENOMEREF -O v |\
+    bcftools norm --threads ${task.cpus} --check-ref s -f $GENOMEREF -O v |\
         awk '{{gsub(/\\y[W|K|Y|R|S|M|B|D|H|V]\\y/,"N",\$4); OFS = "\t"; print}}' |\
         sed '/^\$/d' |\
     bcftools view - -Oz -o  ${sample}.tonly.mut2.norm.vcf.gz
@@ -225,16 +236,18 @@ process mutect2filter_tonly {
 
 
 process varscan_tonly {
+    container "${params.containers.logan}"
+
     label 'process_somaticcaller'
     input:
-        tuple val(tumorname), path(tumor), path(tumorbai), 
+        tuple val(tumorname), path(tumor), path(tumorbai),
         path(bed),
         path(tumorpileup),  path(tumor_con_table)
-    
+
     output:
         tuple val(tumorname),
         path("${tumor.simpleName}_${bed.simpleName}.tonly.varscan.vcf.gz")
-    
+
     shell:
 
     '''
@@ -247,8 +260,8 @@ process varscan_tonly {
     awk '{{gsub(/\\y[W|K|Y|R|S|M|B|D|H|V]\\y/,"N",\$4); OFS = "\t"; print}}' !{tumor.simpleName}_!{bed.simpleName}.tonly.varscan.vcf_temp \
         | sed '/^$/d' | bcftools view - -Oz -o !{tumor.simpleName}_!{bed.simpleName}.tonly.varscan.vcf
 
-    printf "TUMOR\t!{tumorname}\n" > sampname 
-    
+    printf "TUMOR\t!{tumorname}\n" > sampname
+
     bcftools reheader -s sampname !{tumor.simpleName}_!{bed.simpleName}.tonly.varscan.vcf \
         | bcftools view -Oz -o !{tumor.simpleName}_!{bed.simpleName}.tonly.varscan.vcf.gz
 
@@ -263,14 +276,16 @@ process varscan_tonly {
 
 
 process vardict_tonly {
-    label 'process_highcpu'
+    container "${params.containers.logan}"
+    label 'process_somaticcaller_high'
+
     input:
         tuple val(tumorname), path(tumor), path(tumorbai), path(bed)
-    
+
     output:
         tuple val(tumorname),
         path("${tumor.simpleName}_${bed.simpleName}.tonly.vardict.vcf.gz")
-    
+
     script:
 
     """
@@ -281,7 +296,7 @@ process vardict_tonly {
         -x 500 \
         --nosv \
         -b ${tumor} --fisher \
-        -t -Q 20 -c 1 -S 2 -E 3 --th $task.cpus \
+        -t -Q 20 -c 1 -S 2 -E 3 --th ${task.cpus} \
         temp_${bed} | var2vcf_valid.pl \
             -N ${tumor} \
             -Q 20 \
@@ -291,15 +306,15 @@ process vardict_tonly {
             -E \
             -f 0.05 >  ${tumor.simpleName}_${bed.simpleName}.tonly.vardict.vcf
 
-    printf "${tumor.Name}\t${tumorname}\n" > sampname 
-    
+    printf "${tumor.Name}\t${tumorname}\n" > sampname
+
     bcftools reheader -s sampname ${tumor.simpleName}_${bed.simpleName}.tonly.vardict.vcf \
         | bcftools view -Oz -o ${tumor.simpleName}_${bed.simpleName}.tonly.vardict.vcf.gz
 
     """
 
     stub:
-    
+
     """
     touch ${tumor.simpleName}_${bed.simpleName}.tonly.vardict.vcf.gz
 
@@ -309,30 +324,27 @@ process vardict_tonly {
 
 
 process octopus_tonly {
-    //label 'process_highcpu'
+    container "${params.containers.octopus}"
+    label 'process_somaticcaller_high'
 
     input:
         tuple val(tumorname), path(tumor), path(tumorbai), path(bed)
-    
+
     output:
         tuple val(tumorname),
         path("${tumorname}_${bed.simpleName}.tonly.octopus.vcf.gz")
-    
-    script:
 
+    script:
     """
     octopus -R $GENOMEREF -C cancer -I ${tumor} \
     --annotations AC AD DP \
     --target-working-memory 64Gb \
     -t ${bed} \
     $SOMATIC_FOREST \
-    -o ${tumorname}_${bed.simpleName}.tonly.octopus.vcf.gz --threads $task.cpus
-
-
+    -o ${tumorname}_${bed.simpleName}.tonly.octopus.vcf.gz --threads ${task.cpus}
     """
 
     stub:
-    
     """
     touch ${tumorname}_${bed.simpleName}.tonly.octopus.vcf.gz
     """
@@ -341,11 +353,11 @@ process octopus_tonly {
 
 
 process somaticcombine_tonly {
-    label 'process_mid'
-    publishDir(path: "${outdir}/vcfs/combined_tonly", mode: 'copy')
+    container "${params.containers.logan}"
+    label 'process_medium'
 
-    input: 
-        tuple val(tumorsample), 
+    input:
+        tuple val(tumorsample),
         val(callers),
         path(vcfs), path(vcfindex)
 
@@ -376,11 +388,12 @@ process somaticcombine_tonly {
 }
 
 process annotvep_tonly {
-    publishDir("${outdir}/mafs", mode: "copy")
+    container "${params.containers.vcf2maf}"
+    label 'process_medium'
 
     input:
-        tuple val(tumorsample), 
-        val(vc), path(tumorvcf), 
+        tuple val(tumorsample),
+        val(vc), path(tumorvcf),
         path(vcfindex)
 
 
@@ -397,15 +410,15 @@ process annotvep_tonly {
     NORM_VCF_ID_ARG=""
     NSAMPLES=${#VCF_SAMPLE_IDS[@]}
     if [ $NSAMPLES -gt 1 ]; then
-        # Assign tumor, normal IDs 
-        # Look through column names and 
+        # Assign tumor, normal IDs
+        # Look through column names and
         # see if they match provided IDs
         for (( i = 0; i < $NSAMPLES; i++ )); do
             echo "${VCF_SAMPLE_IDS[$i]}"
             if [ "${VCF_SAMPLE_IDS[$i]}" == !{tumorsample} ]; then
                 TID_IDX=$i
             fi
-            
+
         done
 
         if [ ! -z $NID_IDX ]; then
@@ -414,9 +427,9 @@ process annotvep_tonly {
         fi
     fi
     VCF_TID=${VCF_SAMPLE_IDS[$TID_IDX]}
-   
+
     zcat !{tumorvcf} > !{tumorvcf.baseName}
-    
+
     mkdir -p tumor_only/!{vc}
 
     vcf2maf.pl \
@@ -439,9 +452,10 @@ process annotvep_tonly {
 }
 
 process combinemafs_tonly {
+    container "${params.containers.logan}"
     label 'process_low'
 
-    input: 
+    input:
         path(allmafs)
 
     output:
@@ -449,7 +463,7 @@ process combinemafs_tonly {
 
     shell:
     mafin= allmafs.join(" ")
-    
+
     """
     echo "Combining MAFs..."
     head -2 ${allmafs[0]} > final_tonly.maf
@@ -461,6 +475,3 @@ process combinemafs_tonly {
     touch final_tonly.maf
     """
 }
-
-
-
diff --git a/nextflow.config b/nextflow.config
index 70fd5a7..6f66adb 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -7,13 +7,14 @@ manifest {
     mainScript = "main.nf"
 }
 
+
 includeConfig 'conf/containers.config'
 includeConfig 'conf/genomes.config'
 includeConfig 'conf/base.config'
 includeConfig 'conf/modules.config'
 
 
-params { 
+params {
 
     fastq_screen_conf = "${projectDir}/conf/fastq_screen.conf"
     get_flowcell_lanes = "${projectDir}/bin/scripts/flowcell_lane.py"
@@ -23,11 +24,11 @@ params {
     script_ancestry = "${projectDir}/bin/sampleCompareAncestoryPlots.R"
     script_sequenza = "${projectDir}/bin/run_sequenza.R"
     script_freec = "${projectDir}/bin/make_freec_genome.pl"
-    script_freecpaired = "${projectDir}/bin/freec_paired.pl"
+    script_freecpaired = "${projectDir}/bin/make_freec_genome_paired.pl"
     freec_significance = "${projectDir}/bin/assess_significance.R"
     freec_plot = "${projectDir}/bin/makeGraph.R"
     lofreq_convert = "${projectDir}/bin/add_gt_lofreq.sh"
-    split_regions = "24" //Number of regions to split by 
+    split_regions = "24" //Number of regions to split by
 
     vep_cache = "/fdb/VEP/102/cache"
 
@@ -40,10 +41,15 @@ params {
     bam=null
     //Set all Inputs to null
     sample_sheet=null
+
+    fastq_file_input=null
+    bam_file_input=null
+    file_input=null
+
     fastq_input=null
     bam_input=null
+
     BAMINPUT=null
-    file_input=null
 
     publish_dir_mode = 'symlink'
     outdir = 'results'
@@ -67,25 +73,25 @@ profiles {
         autoMounts = true
         cacheDir = "$PWD/singularity"
         envWhitelist='https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOBID'
-        runOptions = '-B /gs10,/gs11,/gs12,/gs9,/spin1,/data/CCBR_Pipeliner/,/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/,/data/nousomedr/,/data/CCBR/projects/,/vf/users,/gpfs,/fdb'
-        }
-    biowulf { 
-        includeConfig 'conf/biowulf.config' 
+        runOptions = '-B /gs10,/gs11,/gs12,/gs9,/spin1,/data/CCBR_Pipeliner/,/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/,/data/CCBR/projects/,/vf/users,/gpfs,/fdb'
+    }
+    biowulf {
+        includeConfig 'conf/biowulf.config'
     }
-    frce { 
-        includeConfig 'conf/frce.config' 
+    frce {
+        includeConfig 'conf/frce.config'
     }
-    interactive { 
-        includeConfig 'conf/interactive.config' 
+    interactive {
+        includeConfig 'conf/interactive.config'
     }
-    slurm { 
-        includeConfig 'conf/slurm.config' 
+    slurm {
+        includeConfig 'conf/slurm.config'
     }
-    ci_stub { 
-        includeConfig 'conf/ci_stub.config' 
+    ci_stub {
+        includeConfig 'conf/ci_stub.config'
     }
 }
-  
+
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
 // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
@@ -99,7 +105,7 @@ profiles {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
-    
+
 
 
 
diff --git a/subworkflows/local/workflows.nf b/subworkflows/local/workflows.nf
index 3e27ff2..766a41a 100644
--- a/subworkflows/local/workflows.nf
+++ b/subworkflows/local/workflows.nf
@@ -71,8 +71,8 @@ workflow INPUT {
 
     if(params.fastq_input){
         fastqinput=Channel.fromFilePairs(params.fastq_input)
-    }else if(params.file_input) {
-        fastqinput=Channel.fromPath(params.file_input)
+    }else if(params.fastq_file_input) {
+        fastqinput=Channel.fromPath(params.fastq_file_input)
                         .splitCsv(header: false, sep: "\t", strip:true)
                         .map{ sample,fq1,fq2 ->
                         tuple(sample, tuple(file(fq1),file(fq2)))
@@ -574,8 +574,8 @@ workflow INPUT_BAM {
             println "Missing BAM Index"
         }
 
-    }else if(params.file_input) {
-        baminputonly=Channel.fromPath(params.file_input)
+    }else if(params.bam_file_input) {
+        baminputonly=Channel.fromPath(params.bam_file_input)
                         .splitCsv(header: false, sep: "\t", strip:true)
                         .map{ sample,bam,bai  ->
                         tuple(sample, file(bam),file(bai))
diff --git a/subworkflows/local/workflows_tonly.nf b/subworkflows/local/workflows_tonly.nf
index c73803a..9f19e1a 100644
--- a/subworkflows/local/workflows_tonly.nf
+++ b/subworkflows/local/workflows_tonly.nf
@@ -51,8 +51,8 @@ workflow INPUT_TONLY {
     if(params.fastq_input){
         fastqinput=Channel.fromFilePairs(params.fastq_input)
 
-    }else if(params.file_input) {
-        fastqinput=Channel.fromPath(params.file_input)
+    }else if(params.fastq_file_input) {
+        fastqinput=Channel.fromPath(params.fastq_file_input)
                         .splitCsv(header: false, sep: "\t", strip:true)
                         .map{ sample,fq1,fq2 -> 
                         tuple(sample, tuple(file(fq1),file(fq2)))
@@ -346,8 +346,8 @@ workflow INPUT_TONLY_BAM {
         sample_sheet=baminputonly.map{samplename,bam,bai -> tuple (
              samplename)}
 
-    }else if(params.file_input) {
-        baminputonly=Channel.fromPath(params.file_input)
+    }else if(params.bam_file_input) {
+        baminputonly=Channel.fromPath(params.bam_file_input)
                         .splitCsv(header: false, sep: "\t", strip:true)
                         .map{ sample,bam,bai  -> 
                         tuple(sample, file(bam),file(bai))