diff --git a/modules/local/BIOMETRICS/biometrics_create_input.nf b/modules/local/BIOMETRICS/biometrics_create_input.nf
index 37ece13..cbf5814 100644
--- a/modules/local/BIOMETRICS/biometrics_create_input.nf
+++ b/modules/local/BIOMETRICS/biometrics_create_input.nf
@@ -1,6 +1,12 @@
 process BIOMETRICS_CREATE_INPUT {
     tag "$patient_id"
     label 'process_single'
+    errorStrategy 'terminate'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6':
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6' }"
 
     input:
     tuple path(patient_json), val(patient_id)
diff --git a/modules/local/BIOMETRICS/biometrics_extract.nf b/modules/local/BIOMETRICS/biometrics_extract.nf
index a92335c..b43d5a7 100644
--- a/modules/local/BIOMETRICS/biometrics_extract.nf
+++ b/modules/local/BIOMETRICS/biometrics_extract.nf
@@ -3,6 +3,9 @@ process BIOMETRICS_EXTRACT {
     label 'biometrics_extract'
 
     conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'ghcr.io/msk-access/biometrics:0.2.16':
+        'ghcr.io/msk-access/biometrics:0.2.16' }"
 
     input:
     tuple val(patient_id), path(biometrics_input)
diff --git a/modules/local/BIOMETRICS/biometrics_genotype.nf b/modules/local/BIOMETRICS/biometrics_genotype.nf
index e28ecd0..25728ac 100644
--- a/modules/local/BIOMETRICS/biometrics_genotype.nf
+++ b/modules/local/BIOMETRICS/biometrics_genotype.nf
@@ -1,7 +1,11 @@
 process BIOMETRICS_GENOTYPE {
     tag "$patient_id"
     label 'biometrics_genotype'
+
     conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'ghcr.io/msk-access/biometrics:0.2.16':
+        'ghcr.io/msk-access/biometrics:0.2.16' }"
 
     input:
     tuple val(patient_id), path(biometrics_input), path(biometrics_extract_db)
diff --git a/modules/local/BIOMETRICS/biometrics_sexmismatch.nf b/modules/local/BIOMETRICS/biometrics_sexmismatch.nf
index 41c11ff..aca48e6 100644
--- a/modules/local/BIOMETRICS/biometrics_sexmismatch.nf
+++ b/modules/local/BIOMETRICS/biometrics_sexmismatch.nf
@@ -1,7 +1,11 @@
 process BIOMETRICS_SEXMISMATCH {
     tag "$patient_id"
     label 'biometrics_genotype'
+
     conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'ghcr.io/msk-access/biometrics:0.2.16':
+        'ghcr.io/msk-access/biometrics:0.2.16' }"
 
     input:
     tuple val(patient_id), path(biometrics_input), path(biometrics_extract_db)
diff --git a/modules/local/BIOMETRICS/biometrics_summary.nf b/modules/local/BIOMETRICS/biometrics_summary.nf
index 2dd1808..ed79eaf 100644
--- a/modules/local/BIOMETRICS/biometrics_summary.nf
+++ b/modules/local/BIOMETRICS/biometrics_summary.nf
@@ -2,6 +2,11 @@ process BIOMETRICS_SUMMARY {
     tag "$patient_id"
     label 'biometrics_summary'
 
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'ghcr.io/msk-access/biometrics:0.2.16':
+        'ghcr.io/msk-access/biometrics:0.2.16' }"
+
     input:
     tuple val(patient_id), path(biometrics_genotype_csv), path(biometrics_sexmismatch_csv)
 
diff --git a/modules/local/COPY_NUMBER/main.nf b/modules/local/COPY_NUMBER/main.nf
index 4dfb4fc..e792b3d 100644
--- a/modules/local/COPY_NUMBER/main.nf
+++ b/modules/local/COPY_NUMBER/main.nf
@@ -2,9 +2,10 @@ process COPY_NUMBER {
     tag "$patient_id"
     label 'process_single'
 
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6':
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6' }"
 
     input:
     tuple path(patient_json), val(patient_id)
diff --git a/modules/local/FIND_FACETS_FIT/main.nf b/modules/local/FIND_FACETS_FIT/main.nf
index c41688e..af32604 100644
--- a/modules/local/FIND_FACETS_FIT/main.nf
+++ b/modules/local/FIND_FACETS_FIT/main.nf
@@ -2,9 +2,10 @@ process FIND_FACETS_FIT {
     tag "$patient_id"
     label 'process_single'
 
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'ghcr.io/msk-access/genotype_variants:0.3.9':
-        'ghcr.io/msk-access/genotype_variants:0.3.9' }"
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6':
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6' }"
 
     input:
     val facets_dir
diff --git a/modules/local/GENERATE_MAF/main.nf b/modules/local/GENERATE_MAF/main.nf
index 1471d0a..0c05871 100644
--- a/modules/local/GENERATE_MAF/main.nf
+++ b/modules/local/GENERATE_MAF/main.nf
@@ -1,9 +1,10 @@
 process GENERATE_MAF {
     label 'process_single'
 
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6':
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6' }"
 
     input:
     path patient_json
diff --git a/modules/local/INFER_SAMPLES/main.nf b/modules/local/INFER_SAMPLES/main.nf
index e31af7e..47727d7 100644
--- a/modules/local/INFER_SAMPLES/main.nf
+++ b/modules/local/INFER_SAMPLES/main.nf
@@ -1,5 +1,11 @@
 process INFER_SAMPLES {
     label 'process_single'
+    errorStrategy 'terminate'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6':
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6' }"
 
     input:
     path id_mapping_file
diff --git a/modules/local/MSI/main.nf b/modules/local/MSI/main.nf
index f468e86..e2f0708 100644
--- a/modules/local/MSI/main.nf
+++ b/modules/local/MSI/main.nf
@@ -2,9 +2,10 @@ process MSI {
     tag "$patient_id"
     label 'process_single'
 
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6':
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6' }"
 
     input:
     tuple path(patient_json), val(patient_id)
diff --git a/modules/local/SNV_INDEL_CREATE_GENOTYPE_INPUT/main.nf b/modules/local/SNV_INDEL_CREATE_GENOTYPE_INPUT/main.nf
index f58404e..1b93a6a 100644
--- a/modules/local/SNV_INDEL_CREATE_GENOTYPE_INPUT/main.nf
+++ b/modules/local/SNV_INDEL_CREATE_GENOTYPE_INPUT/main.nf
@@ -2,9 +2,10 @@ process SNV_INDEL_CREATE_GENOTYPE_INPUT {
     tag "$patient_id"
     label 'process_single'
 
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6':
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6' }"
 
     input:
     tuple path(patient_json), val(patient_id), path(all_calls_maf)
@@ -16,7 +17,7 @@ process SNV_INDEL_CREATE_GENOTYPE_INPUT {
     val clinical_access_unfilter_bam_template
     val clinical_impact_standard_bam_template
 
-//    publishDir "${params.outdir}/intermediate/small_variants/${patient_id}", mode: 'copy', pattern: '*genotyping_input.tsv'
+    publishDir "${params.outdir}/intermediate/small_variants/${patient_id}", mode: 'copy', pattern: '*genotyping_input.tsv'
 
     output:
         tuple path(patient_json), val(patient_id), path("*genotyping_input.tsv"), emit: genotyping_input
diff --git a/modules/local/SNV_INDEL_FILTER_CALLS/main.nf b/modules/local/SNV_INDEL_FILTER_CALLS/main.nf
index 908c739..e51dad3 100644
--- a/modules/local/SNV_INDEL_FILTER_CALLS/main.nf
+++ b/modules/local/SNV_INDEL_FILTER_CALLS/main.nf
@@ -10,6 +10,11 @@ process SNV_INDEL_AGGREGATE_ALLELE_COUNTS {
     label 'process_single'
     tag "${patient_id}"
 
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6':
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6' }"
+
     input:
         tuple path(patient_json), val(patient_id), path(genotyping_output), path(all_small_calls_maf)
         val access_min_cov
@@ -46,6 +51,11 @@ process SNV_INDEL_ANNOTATE_HOTSPOT_CH {
     label 'process_single'
     tag "${patient_id}"
 
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6':
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6' }"
+
     input:
         tuple val(patient_id), path(snv_indel_csv)
         val hotspot_list
@@ -83,6 +93,11 @@ process SNV_INDEL_ADD_FILTER_COL {
     label 'process_single'
     tag "${patient_id}"
 
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6':
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6' }"
+
     input:
         tuple val(patient_id), path(snv_indel_csv)
         val exclude_genes
@@ -131,6 +146,11 @@ process SNV_INDEL_ADD_FACETS_ADJUSTED_VAF {
     label 'process_single'
     tag "${patient_id}"
 
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6':
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6' }"
+
     input:
         tuple val(patient_id), val(sex), path(facets_fit), path(snv_indel_csv)
 
diff --git a/modules/local/SNV_INDEL_GENERATE_UNION_MAF/main.nf b/modules/local/SNV_INDEL_GENERATE_UNION_MAF/main.nf
index 59127bc..3d9ffe3 100644
--- a/modules/local/SNV_INDEL_GENERATE_UNION_MAF/main.nf
+++ b/modules/local/SNV_INDEL_GENERATE_UNION_MAF/main.nf
@@ -2,6 +2,11 @@ process SNV_INDEL_GENERATE_UNION_MAF {
     tag "$patient_id"
     label 'process_single'
 
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6':
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6' }"
+
     input:
     tuple path(patient_json), val(patient_id)
     val research_access_mutations_maf_template
diff --git a/modules/local/SNV_INDEL_GENOTYPE_VARIANTS/main.nf b/modules/local/SNV_INDEL_GENOTYPE_VARIANTS/main.nf
index fe2ba72..fe62e14 100644
--- a/modules/local/SNV_INDEL_GENOTYPE_VARIANTS/main.nf
+++ b/modules/local/SNV_INDEL_GENOTYPE_VARIANTS/main.nf
@@ -1,18 +1,19 @@
 process SNV_INDEL_GENOTYPE_VARIANTS {
     tag "$patient_id"
     label 'genotype_variants'
+    errorStrategy 'terminate'
 
     conda "${moduleDir}/environment.yml"
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'ghcr.io/msk-access/genotype_variants:0.3.9':
-        'ghcr.io/msk-access/genotype_variants:0.3.9' }"
+        'ghcr.io/msk-access/genotype_variants:sha-f0411c85':
+        'ghcr.io/msk-access/genotype_variants:sha-f0411c85' }"
 
     input:
     tuple path(patient_json), val(patient_id), val(genotyping_input)
     val fasta_ref
 
-//    publishDir "${params.outdir}/intermediate/small_variants/${patient_id}/genotyped_mafs", mode: 'copy', pattern: '*.maf'
+    publishDir "${params.outdir}/intermediate/small_variants/${patient_id}/genotyped_mafs", mode: 'copy', pattern: '*.maf'
 
     output:
         tuple path(patient_json), val(patient_id), path("*.maf"), emit: genotyped_mafs
@@ -29,7 +30,7 @@ process SNV_INDEL_GENOTYPE_VARIANTS {
     -i ${genotyping_input} \\
     -r ${fasta_ref} \\
     --filter-duplicate 1 \\
-    -g /work/access/production/resources/tools/GetBaseCountsMultiSample/current/GetBaseCountsMultiSample \\
+    -g /juno/work/access/production/resources/tools/GetBaseCountsMultiSample/current/GetBaseCountsMultiSample \\
     -t ${task.cpus} \\
 
     """
diff --git a/modules/local/STRUCTURAL_VARIANTS/main.nf b/modules/local/STRUCTURAL_VARIANTS/main.nf
index 0a2e3e5..fa13282 100644
--- a/modules/local/STRUCTURAL_VARIANTS/main.nf
+++ b/modules/local/STRUCTURAL_VARIANTS/main.nf
@@ -2,9 +2,10 @@ process STRUCTURAL_VARIANTS {
     tag "$patient_id"
     label 'process_single'
 
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6':
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6' }"
 
     input:
     tuple path(patient_json), val(patient_id)
diff --git a/nextflow.config b/nextflow.config
index f9503cd..554426d 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -10,14 +10,14 @@
 
 // Global default params, used in configs
 params {
-     input = "/juno/cmo/bergerlab/guturus1/testing_cohort/nf_inputs/v2/nf_v2_patients.csv"
-     keep_research_samples_file = "/juno/cmo/bergerlab/guturus1/testing_cohort/nf_inputs/v2/nf_v2_samples.csv" 
+     input = "/juno/cmo/bergerlab/guturus1/testing_cohort/nf_inputs/v1/nf_v1_singularity.csv"
+     keep_research_samples_file = "/juno/cmo/bergerlab/guturus1/testing_cohort/nf_inputs/v1/nf_v1_singularity_samples.csv" 
 //    input = "/juno/cmo/bergerlab/arorak/repositories/clean_copy/access_data_analysis_nf/assets/test_accessv2_input.csv"
 //    keep_research_samples_file	  = "/juno/cmo/bergerlab/arorak/repositories/clean_copy/access_data_analysis_nf/assets/test_accessv2_include.csv"
     exclude_samples_file          = null
 
     // Output dir
-    outdir			  = "./results_accessv2/biometrics_only/"
+    outdir			  = "/juno/cmo/bergerlab/guturus1/testing_cohort/nf_outputs/v1/singularity"
 
     variant_filter_rules = [
     exclude_genes           : "RP11-",
@@ -117,9 +117,9 @@ profiles {
         apptainer.enabled       = false
     }
     docker {
-        docker.enabled          = true
+        docker.enabled          = false
         conda.enabled           = false
-        singularity.enabled     = false
+        singularity.enabled     = true
         podman.enabled          = false
         shifter.enabled         = false
         charliecloud.enabled    = false
@@ -132,6 +132,7 @@ profiles {
     singularity {
         singularity.enabled     = true
         singularity.autoMounts  = true
+        singularity.runOptions  = '--bind /juno/:/juno/'
         conda.enabled           = false
         docker.enabled          = false
         podman.enabled          = false