From 377c778170ba37cf579e83fcaa93a5188724c491 Mon Sep 17 00:00:00 2001
From: Shivani Guturu <shguturu@gmail.com>
Date: Tue, 28 Oct 2025 09:17:00 -0400
Subject: [PATCH 1/4] singularity config

---
 modules/local/COPY_NUMBER/main.nf             |  4 ---
 modules/local/FIND_FACETS_FIT/main.nf         |  4 ---
 modules/local/GENERATE_MAF/main.nf            |  4 ---
 modules/local/MSI/main.nf                     |  4 ---
 .../SNV_INDEL_CREATE_GENOTYPE_INPUT/main.nf   |  4 ---
 .../local/SNV_INDEL_GENOTYPE_VARIANTS/main.nf |  4 ---
 modules/local/STRUCTURAL_VARIANTS/main.nf     |  4 ---
 nextflow.config                               | 25 ++++++++++++++++---
 8 files changed, 22 insertions(+), 31 deletions(-)

diff --git a/modules/local/COPY_NUMBER/main.nf b/modules/local/COPY_NUMBER/main.nf
index 4dfb4fc..7201f67 100644
--- a/modules/local/COPY_NUMBER/main.nf
+++ b/modules/local/COPY_NUMBER/main.nf
@@ -2,10 +2,6 @@ process COPY_NUMBER {
     tag "$patient_id"
     label 'process_single'
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
-
     input:
     tuple path(patient_json), val(patient_id)
     val research_access_cna_template
diff --git a/modules/local/FIND_FACETS_FIT/main.nf b/modules/local/FIND_FACETS_FIT/main.nf
index c41688e..9ff7b33 100644
--- a/modules/local/FIND_FACETS_FIT/main.nf
+++ b/modules/local/FIND_FACETS_FIT/main.nf
@@ -2,10 +2,6 @@ process FIND_FACETS_FIT {
     tag "$patient_id"
     label 'process_single'
 
-    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' }"
-
     input:
     val facets_dir
     tuple path(patient_json), val(patient_id)
diff --git a/modules/local/GENERATE_MAF/main.nf b/modules/local/GENERATE_MAF/main.nf
index 1471d0a..ae32a32 100644
--- a/modules/local/GENERATE_MAF/main.nf
+++ b/modules/local/GENERATE_MAF/main.nf
@@ -1,10 +1,6 @@
 process GENERATE_MAF {
     label 'process_single'
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
-
     input:
     path patient_json
     val research_access_mutations_maf_template
diff --git a/modules/local/MSI/main.nf b/modules/local/MSI/main.nf
index f468e86..52e45c0 100644
--- a/modules/local/MSI/main.nf
+++ b/modules/local/MSI/main.nf
@@ -2,10 +2,6 @@ process MSI {
     tag "$patient_id"
     label 'process_single'
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
-
     input:
     tuple path(patient_json), val(patient_id)
     val reseach_access_msi_template
diff --git a/modules/local/SNV_INDEL_CREATE_GENOTYPE_INPUT/main.nf b/modules/local/SNV_INDEL_CREATE_GENOTYPE_INPUT/main.nf
index f58404e..3dbe384 100644
--- a/modules/local/SNV_INDEL_CREATE_GENOTYPE_INPUT/main.nf
+++ b/modules/local/SNV_INDEL_CREATE_GENOTYPE_INPUT/main.nf
@@ -2,10 +2,6 @@ process SNV_INDEL_CREATE_GENOTYPE_INPUT {
     tag "$patient_id"
     label 'process_single'
 
-    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' }"
-
     input:
     tuple path(patient_json), val(patient_id), path(all_calls_maf)
     val research_access_duplex_bam_template
diff --git a/modules/local/SNV_INDEL_GENOTYPE_VARIANTS/main.nf b/modules/local/SNV_INDEL_GENOTYPE_VARIANTS/main.nf
index fe2ba72..7757bdf 100644
--- a/modules/local/SNV_INDEL_GENOTYPE_VARIANTS/main.nf
+++ b/modules/local/SNV_INDEL_GENOTYPE_VARIANTS/main.nf
@@ -4,10 +4,6 @@ process SNV_INDEL_GENOTYPE_VARIANTS {
 
     conda "${moduleDir}/environment.yml"
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'ghcr.io/msk-access/genotype_variants:0.3.9':
-        'ghcr.io/msk-access/genotype_variants:0.3.9' }"
-
     input:
     tuple path(patient_json), val(patient_id), val(genotyping_input)
     val fasta_ref
diff --git a/modules/local/STRUCTURAL_VARIANTS/main.nf b/modules/local/STRUCTURAL_VARIANTS/main.nf
index 0a2e3e5..fbbafe6 100644
--- a/modules/local/STRUCTURAL_VARIANTS/main.nf
+++ b/modules/local/STRUCTURAL_VARIANTS/main.nf
@@ -2,10 +2,6 @@ process STRUCTURAL_VARIANTS {
     tag "$patient_id"
     label 'process_single'
 
-    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' }"
-
     input:
     tuple path(patient_json), val(patient_id)
     val research_access_sv_template
diff --git a/nextflow.config b/nextflow.config
index f9503cd..ba8faac 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -117,27 +117,46 @@ 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
         apptainer.enabled       = false
         docker.runOptions       = '-u $(id -u):$(id -g)'
+        process {
+            container = '/singularity_cache/jupyter-scipy-notebook-python-3.9.sif'
+            withLabel: 'genotype_variants' {
+                container = './singularity_cache/genotype_variants-0.3.10.sif'
+            }
+            withLabel: 'biometrics' {
+                container = './singularity_cache/biometrics-0.2.16.sif'
+            }
+        }
     }
     arm {
         docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
         singularity.enabled     = true
-        singularity.autoMounts  = true
+        singularity.autoMounts  = false
+        singularity.runOptions  = '--bind /juno:/juno,/scratch:/scratch -u $(id -u):$(id -g) --disable-overlay --debug'
         conda.enabled           = false
         docker.enabled          = false
         podman.enabled          = false
         shifter.enabled         = false
         charliecloud.enabled    = false
         apptainer.enabled       = false
+        process {
+            container = '/juno/cmo/bergerlab/guturus1/oct/access_data_analysis_nf/singularity_cache/jupyter-scipy-notebook-python-3.9.sif'
+            withLabel: 'genotype_variants' {
+                container = '/juno/cmo/bergerlab/guturus1/oct/access_data_analysis_nf/singularity_cache/genotype_variants-0.3.10.sif'
+            }
+            withLabel: 'biometrics' {
+                container = '/juno/cmo/bergerlab/guturus1/oct/access_data_analysis_nf/singularity_cache/biometrics-0.2.16.sif'
+            }
+        }
     }
     podman {
         podman.enabled          = true

From eeecf94098ff0188a199f407ed66dc510d07d6af Mon Sep 17 00:00:00 2001
From: Shivani Guturu <shguturu@gmail.com>
Date: Thu, 30 Oct 2025 11:45:06 -0400
Subject: [PATCH 2/4] testing msk containers

---
 .../BIOMETRICS/biometrics_create_input.nf     |  6 ++
 .../local/BIOMETRICS/biometrics_extract.nf    |  3 +
 .../local/BIOMETRICS/biometrics_genotype.nf   |  4 ++
 .../BIOMETRICS/biometrics_sexmismatch.nf      |  4 ++
 .../local/BIOMETRICS/biometrics_summary.nf    |  5 ++
 modules/local/COPY_NUMBER/main.nf             |  5 ++
 modules/local/FIND_FACETS_FIT/main.nf         |  5 ++
 modules/local/GENERATE_MAF/main.nf            |  5 ++
 modules/local/GENOTYPE_VARIANTS/main.nf       | 67 +++++++++++++++++++
 modules/local/INFER_SAMPLES/main.nf           |  6 ++
 modules/local/MSI/main.nf                     |  5 ++
 .../SNV_INDEL_CREATE_GENOTYPE_INPUT/main.nf   |  7 +-
 modules/local/SNV_INDEL_FILTER_CALLS/main.nf  | 20 ++++++
 .../SNV_INDEL_GENERATE_UNION_MAF/main.nf      |  5 ++
 .../local/SNV_INDEL_GENOTYPE_VARIANTS/main.nf |  9 ++-
 modules/local/STRUCTURAL_VARIANTS/main.nf     |  5 ++
 nextflow.config                               | 10 +--
 17 files changed, 163 insertions(+), 8 deletions(-)
 create mode 100644 modules/local/GENOTYPE_VARIANTS/main.nf

diff --git a/modules/local/BIOMETRICS/biometrics_create_input.nf b/modules/local/BIOMETRICS/biometrics_create_input.nf
index 37ece13..67512a0 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/biometrics:0.2.16':
+        'ghcr.io/msk-access/biometrics:0.2.16' }"
 
     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 7201f67..e792b3d 100644
--- a/modules/local/COPY_NUMBER/main.nf
+++ b/modules/local/COPY_NUMBER/main.nf
@@ -2,6 +2,11 @@ process COPY_NUMBER {
     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_cna_template
diff --git a/modules/local/FIND_FACETS_FIT/main.nf b/modules/local/FIND_FACETS_FIT/main.nf
index 9ff7b33..af32604 100644
--- a/modules/local/FIND_FACETS_FIT/main.nf
+++ b/modules/local/FIND_FACETS_FIT/main.nf
@@ -2,6 +2,11 @@ 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/postprocessing_variant_calls:0.2.6':
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6' }"
+
     input:
     val facets_dir
     tuple path(patient_json), val(patient_id)
diff --git a/modules/local/GENERATE_MAF/main.nf b/modules/local/GENERATE_MAF/main.nf
index ae32a32..0c05871 100644
--- a/modules/local/GENERATE_MAF/main.nf
+++ b/modules/local/GENERATE_MAF/main.nf
@@ -1,6 +1,11 @@
 process GENERATE_MAF {
     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:
     path patient_json
     val research_access_mutations_maf_template
diff --git a/modules/local/GENOTYPE_VARIANTS/main.nf b/modules/local/GENOTYPE_VARIANTS/main.nf
new file mode 100644
index 0000000..252afd7
--- /dev/null
+++ b/modules/local/GENOTYPE_VARIANTS/main.nf
@@ -0,0 +1,67 @@
+process GENOTYPEVARIANTS_ALL {
+    tag "$meta.id"
+    label 'process_medium'
+    errorStrategy 'terminate'
+
+    conda "${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' }"
+
+    input:
+    // [[patient:null, id:'sample'], standard.bam, standard.bam.bai, [], [], [], []]
+    // or
+    // [[patient:null, id:'sample'], [], [], duplex.bam, duplex.bam.bai, simplex.bam, simplex.bam.bai]
+    tuple val(meta), path(bam_standard), path(bai_standard), path(bam_duplex), path(bai_duplex), path(bam_simplex), path(bai_simplex), path(maf)
+    path(fasta)
+    path(fai)
+
+    output:
+    tuple val(meta), path("*.maf"), emit: maf
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def sample = task.ext.prefix != null ? "-si ${task.ext.prefix}" : (meta.id != null ? "-si ${meta.id}" : "")
+    def patient = meta.patient ?"-p ${meta.patient}": ''
+    def bams_standard = bam_standard ?"-b $bam_standard" : ''
+    def bam_liquid = (bam_duplex && bam_simplex) ? "-d $bam_duplex -s $bam_simplex" : ''
+
+    """
+    genotype_variants small_variants all \\
+    -i ${maf} \\
+    -r ${fasta} \\
+    -g /usr/local/bin/GetBaseCountsMultiSample \\
+    $patient \\
+    $bams_standard \\
+    $bam_liquid \\
+    $sample \\
+    $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        genotypevariants: \$(genotype_variants --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def sample = "${meta.sample}"
+    def patient = "${meta.patient}"
+
+    """
+    touch ${prefix}-DUPLEX_genotyped.maf
+    touch ${prefix}-ORG-SIMPLEX-DUPLEX_genotyped.maf
+    touch ${prefix}-SIMPLEX-DUPLEX_genotyped.maf
+    touch ${prefix}-SIMPLEX_genotyped.maf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        genotypevariants: \$(genotype_variants --version)
+    END_VERSIONS
+    """
+}
\ No newline at end of file
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 52e45c0..e2f0708 100644
--- a/modules/local/MSI/main.nf
+++ b/modules/local/MSI/main.nf
@@ -2,6 +2,11 @@ process MSI {
     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 reseach_access_msi_template
diff --git a/modules/local/SNV_INDEL_CREATE_GENOTYPE_INPUT/main.nf b/modules/local/SNV_INDEL_CREATE_GENOTYPE_INPUT/main.nf
index 3dbe384..1b93a6a 100644
--- a/modules/local/SNV_INDEL_CREATE_GENOTYPE_INPUT/main.nf
+++ b/modules/local/SNV_INDEL_CREATE_GENOTYPE_INPUT/main.nf
@@ -2,6 +2,11 @@ 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 ?
+        '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)
     val research_access_duplex_bam_template
@@ -12,7 +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 7757bdf..fe62e14 100644
--- a/modules/local/SNV_INDEL_GENOTYPE_VARIANTS/main.nf
+++ b/modules/local/SNV_INDEL_GENOTYPE_VARIANTS/main.nf
@@ -1,14 +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: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
@@ -25,7 +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 fbbafe6..fa13282 100644
--- a/modules/local/STRUCTURAL_VARIANTS/main.nf
+++ b/modules/local/STRUCTURAL_VARIANTS/main.nf
@@ -2,6 +2,11 @@ process STRUCTURAL_VARIANTS {
     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_sv_template
diff --git a/nextflow.config b/nextflow.config
index ba8faac..71a17fe 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-",
@@ -140,8 +140,8 @@ profiles {
     }
     singularity {
         singularity.enabled     = true
-        singularity.autoMounts  = false
-        singularity.runOptions  = '--bind /juno:/juno,/scratch:/scratch -u $(id -u):$(id -g) --disable-overlay --debug'
+        singularity.autoMounts  = true
+        singularity.runOptions  = '--bind /juno/:/juno/'
         conda.enabled           = false
         docker.enabled          = false
         podman.enabled          = false

From ef0398d809847bde1d9ddf92d90a63c9138da117 Mon Sep 17 00:00:00 2001
From: Shivani Guturu <shguturu@gmail.com>
Date: Thu, 30 Oct 2025 12:16:23 -0400
Subject: [PATCH 3/4] remove generic container options

---
 modules/local/GENOTYPE_VARIANTS/main.nf | 67 -------------------------
 nextflow.config                         | 18 -------
 2 files changed, 85 deletions(-)
 delete mode 100644 modules/local/GENOTYPE_VARIANTS/main.nf

diff --git a/modules/local/GENOTYPE_VARIANTS/main.nf b/modules/local/GENOTYPE_VARIANTS/main.nf
deleted file mode 100644
index 252afd7..0000000
--- a/modules/local/GENOTYPE_VARIANTS/main.nf
+++ /dev/null
@@ -1,67 +0,0 @@
-process GENOTYPEVARIANTS_ALL {
-    tag "$meta.id"
-    label 'process_medium'
-    errorStrategy 'terminate'
-
-    conda "${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' }"
-
-    input:
-    // [[patient:null, id:'sample'], standard.bam, standard.bam.bai, [], [], [], []]
-    // or
-    // [[patient:null, id:'sample'], [], [], duplex.bam, duplex.bam.bai, simplex.bam, simplex.bam.bai]
-    tuple val(meta), path(bam_standard), path(bai_standard), path(bam_duplex), path(bai_duplex), path(bam_simplex), path(bai_simplex), path(maf)
-    path(fasta)
-    path(fai)
-
-    output:
-    tuple val(meta), path("*.maf"), emit: maf
-    path "versions.yml"           , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def sample = task.ext.prefix != null ? "-si ${task.ext.prefix}" : (meta.id != null ? "-si ${meta.id}" : "")
-    def patient = meta.patient ?"-p ${meta.patient}": ''
-    def bams_standard = bam_standard ?"-b $bam_standard" : ''
-    def bam_liquid = (bam_duplex && bam_simplex) ? "-d $bam_duplex -s $bam_simplex" : ''
-
-    """
-    genotype_variants small_variants all \\
-    -i ${maf} \\
-    -r ${fasta} \\
-    -g /usr/local/bin/GetBaseCountsMultiSample \\
-    $patient \\
-    $bams_standard \\
-    $bam_liquid \\
-    $sample \\
-    $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        genotypevariants: \$(genotype_variants --version)
-    END_VERSIONS
-    """
-
-    stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def sample = "${meta.sample}"
-    def patient = "${meta.patient}"
-
-    """
-    touch ${prefix}-DUPLEX_genotyped.maf
-    touch ${prefix}-ORG-SIMPLEX-DUPLEX_genotyped.maf
-    touch ${prefix}-SIMPLEX-DUPLEX_genotyped.maf
-    touch ${prefix}-SIMPLEX_genotyped.maf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        genotypevariants: \$(genotype_variants --version)
-    END_VERSIONS
-    """
-}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 71a17fe..554426d 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -125,15 +125,6 @@ profiles {
         charliecloud.enabled    = false
         apptainer.enabled       = false
         docker.runOptions       = '-u $(id -u):$(id -g)'
-        process {
-            container = '/singularity_cache/jupyter-scipy-notebook-python-3.9.sif'
-            withLabel: 'genotype_variants' {
-                container = './singularity_cache/genotype_variants-0.3.10.sif'
-            }
-            withLabel: 'biometrics' {
-                container = './singularity_cache/biometrics-0.2.16.sif'
-            }
-        }
     }
     arm {
         docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
@@ -148,15 +139,6 @@ profiles {
         shifter.enabled         = false
         charliecloud.enabled    = false
         apptainer.enabled       = false
-        process {
-            container = '/juno/cmo/bergerlab/guturus1/oct/access_data_analysis_nf/singularity_cache/jupyter-scipy-notebook-python-3.9.sif'
-            withLabel: 'genotype_variants' {
-                container = '/juno/cmo/bergerlab/guturus1/oct/access_data_analysis_nf/singularity_cache/genotype_variants-0.3.10.sif'
-            }
-            withLabel: 'biometrics' {
-                container = '/juno/cmo/bergerlab/guturus1/oct/access_data_analysis_nf/singularity_cache/biometrics-0.2.16.sif'
-            }
-        }
     }
     podman {
         podman.enabled          = true

From d016be2e643b37e4aaaa1edb759fce2de7debaf9 Mon Sep 17 00:00:00 2001
From: Shivani Guturu <shguturu@gmail.com>
Date: Tue, 4 Nov 2025 12:21:23 -0500
Subject: [PATCH 4/4] biometrics create input doesn't need biometrics container

---
 modules/local/BIOMETRICS/biometrics_create_input.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/BIOMETRICS/biometrics_create_input.nf b/modules/local/BIOMETRICS/biometrics_create_input.nf
index 67512a0..cbf5814 100644
--- a/modules/local/BIOMETRICS/biometrics_create_input.nf
+++ b/modules/local/BIOMETRICS/biometrics_create_input.nf
@@ -5,8 +5,8 @@ process BIOMETRICS_CREATE_INPUT {
 
     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' }"
+        '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)