scholl-lab/sm-calling

None

Overview

Latest release: v1.5.3, Last update: 2026-10-20

Share link: https://snakemake.github.io/snakemake-workflow-catalog?wf=scholl-lab/sm-calling

Quality control: linting: failed formatting: failed

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Conda package manager. It is recommended to install conda via Miniforge. Run

conda create -c conda-forge -c bioconda -c nodefaults --name snakemake snakemake snakedeploy

to install both Snakemake and Snakedeploy in an isolated environment. For all following commands ensure that this environment is activated via

conda activate snakemake

For other installation methods, refer to the Snakemake and Snakedeploy documentation.

Step 2: Deploy workflow

With Snakemake and Snakedeploy installed, the workflow can be deployed as follows. First, create an appropriate project working directory on your system and enter it:

mkdir -p path/to/project-workdir
cd path/to/project-workdir

In all following steps, we will assume that you are inside of that directory. Then run

snakedeploy deploy-workflow https://github.com/scholl-lab/sm-calling . --tag v1.5.3

Snakedeploy will create two folders, workflow and config. The former contains the deployment of the chosen workflow as a Snakemake module, the latter contains configuration files which will be modified in the next step in order to configure the workflow to your needs.

Step 3: Configure workflow

To configure the workflow, adapt config/config.yml to your needs following the instructions below.

Step 4: Run workflow

The deployment method is controlled using the --software-deployment-method (short --sdm) argument.

To run the workflow with automatic deployment of all required software via conda/mamba, use

snakemake --cores all --sdm conda

Snakemake will automatically detect the main Snakefile in the workflow subfolder and execute the workflow module that has been defined by the deployment in step 2.

For further options such as cluster and cloud execution, see the docs.

Step 5: Generate report

After finalizing your data analysis, you can automatically generate an interactive visual HTML report for inspection of results together with parameters and code inside of the browser using

snakemake --report report.zip

Configuration

The following section is imported from the workflow’s config/README.md.

Configuration

config.yaml

Unified pipeline configuration. All paths are relative to the repository root.

Required Fields

Field

Type

Description

caller

string

"mutect2", "freebayes", or "all"

ref.genome

string

Path to reference genome FASTA

ref.build

string

"GRCh37" or "GRCh38"

paths.samples

string

Path to samples TSV

paths.bam_folder

string

Directory with input BAMs

paths.output_folder

string

Root output directory

bam.file_extension

string

BAM file suffix (e.g., .merged.dedup.bqsr.bam)

scatter.mode

string

"chromosome", "interval", or "none"

Required for Mutect2

Field

Description

gatk_resources.panel_of_normals

Path to prebuilt Panel of Normals VCF (or "" to build a cohort PoN from normals)

gatk_resources.extra_panel_of_normals

Optional sites-only PoN VCF (e.g. 1000g_pon.hg38.vcf.gz) merged with the cohort PoN before hotspot masking

gatk_resources.pon_mask_bed

Optional BED of recurrent somatic hotspot regions masked out of the cohort/combined PoN

gatk_resources.af_only_gnomad

Path to gnomAD allele frequency VCF

gatk_resources.common_biallelic_gnomad

Path to gnomAD common biallelic VCF

Mutect2 Parameters (params.mutect2)

Field

Type

Default

Description

genotype_germline_sites

boolean

true

Emit germline sites (required for PureCN)

genotype_pon_sites

boolean

true

Emit PoN sites (required for PureCN)

annotations

array of strings

[]

Extra --annotation flags for Mutect2

annotation_groups

array of strings

[]

Extra --annotation-group flags for Mutect2

extra

string

""

Passthrough for any other Mutect2 flags

QC Parameters (params.bcftools_stats)

Field

Type

Default

Description

extra

string

""

Extra flags for bcftools stats

PureCN Settings (purecn)

Field

Type

Default

Description

enabled

boolean

false

Enable PureCN copy number analysis

genome

string

"hg38"

PureCN genome identifier ("hg19" or "hg38")

intervals_bed

string

""

BED file with capture bait coordinates

normaldb

string

""

Pre-built normalDB.rds (skip NormalDB.R if provided)

mapping_bias

string

""

Pre-built mapping_bias.rds

snp_blacklist

string

""

Optional simple repeats BED for SNP filtering

extra

string

""

Extra PureCN.R arguments

seed

integer

123

Random seed for PureCN

postoptimize

boolean

true

Run PureCN post-optimization

samples.tsv

Tab-separated sample metadata. Required columns:

Column

Description

sample

Unique sample/analysis identifier

tumor_bam

BAM file basename (without extension)

normal_bam

Matched normal BAM basename, or . if none

analysis_type

tumor_only, tumor_normal, or germline

Workflow parameters

The following table is automatically parsed from the workflow’s config.schema.y(a)ml file.

Parameter

Type

Description

Required

Default

caller

string

Which variant caller(s) to run.

yes

ref

yes

. genome

string

Path to reference genome FASTA.

yes

. build

string

Reference genome build identifier.

yes

gatk_resources

GATK resource files. Required for Mutect2, optional for FreeBayes-only runs.

. panel_of_normals

string

yes

. extra_panel_of_normals

string

. pon_mask_bed

string

. af_only_gnomad

string

yes

. common_biallelic_gnomad

string

yes

paths

yes

. samples

string

Path to the samples TSV file.

yes

. bam_folder

string

Directory containing input BAM files.

yes

. output_folder

string

Root directory for pipeline outputs.

yes

. log_subdir

string

logs

. intervals_dir

string

analysis/intervals

bam

yes

. file_extension

string

yes

.merged.dedup.bqsr.bam

scatter

yes

. mode

string

yes

. count

integer

400

. target_bed

string

Optional capture target BED file for interval restriction.

. chromosomes

array

params

. mutect2

. . genotype_germline_sites

boolean

Emit germline sites (required for PureCN).

true

. . genotype_pon_sites

boolean

Emit PoN sites (required for PureCN).

true

. . disable_adaptive_pruning

boolean

Disable Mutect2 adaptive pruning to prevent silent dropout of low-AF somatic variants in tumor-normal mode (GATK issue #7232).

true

. . annotations

array

Extra –annotation flags for Mutect2.

[]

. . annotation_groups

array

Extra –annotation-group flags for Mutect2.

[]

. . extra

string

. filter_mutect_calls

. . extra

string

. freebayes

. bcftools_norm

. bcftools_stats

. . extra

string

purecn

. enabled

boolean

Enable PureCN copy number analysis.

false

. genome

string

PureCN genome identifier.

hg38

. intervals_bed

string

BED file with capture bait coordinates.

. normaldb

string

Pre-built normalDB.rds (skip NormalDB.R if provided).

. mapping_bias

string

Pre-built mapping_bias.rds.

. snp_blacklist

string

Optional simple repeats BED for SNP filtering.

. extra

string

Extra PureCN.R arguments.

. seed

integer

Random seed for PureCN.

123

. postoptimize

boolean

Run PureCN post-optimization.

true

Linting and formatting

Linting results
 1/home/runner/work/snakemake-workflow-catalog/snakemake-workflow-catalog/.pixi/envs/default/lib/python3.13/site-packages/google/auth/transport/grpc.py:43: FutureWarning: grpcio < 1.83.0 does not support Post-Quantum Cryptography (PQC). Support for non-PQC environments is deprecated. In April 2027, google-auth will raise its minimum requirements to enforce grpcio >= 1.83.0. For more details on Google Cloud's post-quantum security migration, visit: https://cloud.google.com/security/resources/post-quantum-cryptography
 2  warnings.warn(
 3Using workflow specific profile profiles/default for setting default command line arguments.
 4Lints for snakefile /tmp/tmp6rri4s2_/scholl-lab-sm-calling-8a7d3c4/workflow/rules/mutect2.smk:
 5    * Absolute path "/^@RG/ {{s=""; for (i=1; i<=NF; i++) if ($i ~ /^SM:/) s=substr($i, 4); print s}}" in line 350:
 6      Do not define absolute paths inside of the workflow, since this renders
 7      your workflow irreproducible on other machines. Use path relative to the
 8      working directory instead, or make the path configurable via a config
 9      file.
10      Also see:
11      https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
12
13Lints for snakefile /tmp/tmp6rri4s2_/scholl-lab-sm-calling-8a7d3c4/workflow/rules/freebayes.smk:
14    * Mixed rules and functions in same snakefile.:
15      Small one-liner functions used only once should be defined as lambda
16      expressions. Other functions should be collected in a common module, e.g.
17      'rules/common.smk'. This makes the workflow steps more readable.
18      Also see:
19      https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
20
21Lints for snakefile /tmp/tmp6rri4s2_/scholl-lab-sm-calling-8a7d3c4/workflow/rules/purecn.smk:
22    * Mixed rules and functions in same snakefile.:
23      Small one-liner functions used only once should be defined as lambda
24      expressions. Other functions should be collected in a common module, e.g.
25      'rules/common.smk'. This makes the workflow steps more readable.
26      Also see:
27      https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
28
29Lints for rule merge_freebayes_vcfs (line 58, /tmp/tmp6rri4s2_/scholl-lab-sm-calling-8a7d3c4/workflow/rules/freebayes.smk):
30    * Shell command directly uses variable REF from outside of the rule:
31      It is recommended to pass all files as input and output, and non-file
32      parameters via the params directive. Otherwise, provenance tracking is
33      less accurate.
34      Also see:
35      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
Formatting results
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 6[DEBUG] In file "/tmp/tmp6rri4s2_/scholl-lab-sm-calling-8a7d3c4/workflow/rules/purecn.smk":  Formatted content is different from original
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 8[DEBUG] In file "/tmp/tmp6rri4s2_/scholl-lab-sm-calling-8a7d3c4/workflow/rules/mutect2.smk":  Formatted content is different from original
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10[INFO] 2 file(s) would be changed 😬
11[INFO] 5 file(s) would be left unchanged 🎉
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13snakefmt version: 0.11.5