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Singularity profile #31

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377c778
singularity config
shguturu Oct 28, 2025
eeecf94
testing msk containers
shguturu Oct 30, 2025
ef0398d
remove generic container options
shguturu Oct 30, 2025
d016be2
biometrics create input doesn't need biometrics container
shguturu Nov 4, 2025
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6 changes: 6 additions & 0 deletions modules/local/BIOMETRICS/biometrics_create_input.nf
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@@ -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)
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3 changes: 3 additions & 0 deletions modules/local/BIOMETRICS/biometrics_extract.nf
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Expand Up @@ -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)
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4 changes: 4 additions & 0 deletions modules/local/BIOMETRICS/biometrics_genotype.nf
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@@ -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)
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4 changes: 4 additions & 0 deletions modules/local/BIOMETRICS/biometrics_sexmismatch.nf
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@@ -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)
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5 changes: 5 additions & 0 deletions modules/local/BIOMETRICS/biometrics_summary.nf
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Expand Up @@ -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)

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5 changes: 3 additions & 2 deletions modules/local/COPY_NUMBER/main.nf
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Expand Up @@ -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)
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5 changes: 3 additions & 2 deletions modules/local/FIND_FACETS_FIT/main.nf
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Expand Up @@ -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
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5 changes: 3 additions & 2 deletions modules/local/GENERATE_MAF/main.nf
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@@ -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
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6 changes: 6 additions & 0 deletions modules/local/INFER_SAMPLES/main.nf
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@@ -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
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5 changes: 3 additions & 2 deletions modules/local/MSI/main.nf
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Expand Up @@ -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)
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7 changes: 4 additions & 3 deletions modules/local/SNV_INDEL_CREATE_GENOTYPE_INPUT/main.nf
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Expand Up @@ -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)
Expand All @@ -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
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20 changes: 20 additions & 0 deletions modules/local/SNV_INDEL_FILTER_CALLS/main.nf
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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)

Expand Down
5 changes: 5 additions & 0 deletions modules/local/SNV_INDEL_GENERATE_UNION_MAF/main.nf
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Expand Up @@ -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
Expand Down
9 changes: 5 additions & 4 deletions modules/local/SNV_INDEL_GENOTYPE_VARIANTS/main.nf
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@@ -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
Expand All @@ -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} \\

"""
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5 changes: 3 additions & 2 deletions modules/local/STRUCTURAL_VARIANTS/main.nf
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Expand Up @@ -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)
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11 changes: 6 additions & 5 deletions nextflow.config
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Expand Up @@ -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-",
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand Down