martykardos/asacphus_fire_frogs

Genomic analysis of Ascaphus thermal tolerance

Overview

Latest release: None, Last update: 2026-07-20

Share link: https://snakemake.github.io/snakemake-workflow-catalog?wf=martykardos/asacphus_fire_frogs

Quality control: linting: failed formatting: failed

Wrappers: bio/bcftools/stats bio/gatk/combinegvcfs bio/gatk/genomicsdbimport bio/gatk/genotypegvcfs bio/gatk/haplotypecaller bio/gatk/variantfiltration bio/multiqc bio/picard/collectmultiplemetrics bio/picard/markduplicates bio/picard/mergevcfs bio/reference/ensembl-sequence bio/reference/ensembl-variation bio/samtools/merge bio/samtools/mpileup bio/snpeff/annotate bio/snpeff/download bio/trimmomatic/pe bio/trimmomatic/se bio/vep/annotate

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/martykardos/asacphus_fire_frogs . --tag None

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.

Configuring grenepipe

Grenepipe is a highly flexible workflow for variant calling from raw sample sequences, with lots of bells and whistles. To configure this workflow, modify config/config.yaml according to your needs, following the explanations provided in the file.

Furthermore, for the general usage of grenepipe, see our wiki. See there to get started with grenepipe.

Pipeline Overview

Minimal input:

  • Reference genome fasta file

  • Per-sample fastq files

  • Optionally, a vcf file of known variants to restrict the variant calling process

Process and available tools:

Typical output:

  • Variant calls vcf, raw and filtered, and potentially with annotations

  • MultiQC report (includes summaries of most other tools, and of the final vcf)

  • Snakemake report (optional)

Workflow parameters

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

Parameter

Type

Description

Required

Default

data

yes

. samples-table

string

yes

. samples-count

integer

. reference-genome

string

yes

. known-variants

string

yes

settings

yes

. trimming-tool

string

yes

. merge-paired-end-reads

boolean

yes

. mapping-tool

string

yes

. filter-mapped-reads

boolean

yes

. clip-read-overlaps

boolean

yes

. remove-duplicates

boolean

yes

. duplicates-tool

string

yes

. recalibrate-base-qualities

boolean

yes

. calling-tool

string

yes

. restrict-regions

string

yes

. contig-group-size

integer

yes

. filter-variants

string

. keep-intermediate

. . trimming

boolean

. . mapping

boolean

. . calling

boolean

. snpeff

boolean

yes

. vep

boolean

yes

. mapdamage

boolean

yes

. damageprofiler

boolean

yes

. pileups

[‘array’]

yes

. hafpipe

boolean

yes

. frequency-table

boolean

yes

params

yes

. adapterremoval

yes

. . threads

integer

. . se

string

. . pe

string

. cutadapt

yes

. . threads

integer

. . se

. . pe

. fastp

yes

. . threads

integer

. . se

string

. . pe

string

. seqprep

yes

. . extra

string

. skewer

yes

. . threads

integer

. . se

string

. . pe

string

. trimmomatic

yes

. . threads

integer

. . se

. . pe

. bowtie2

yes

. . threads

integer

. . extra

string

. bwaaln

yes

. . threads

integer

. . extra

string

. . extra-sort

string

. bwamem

yes

. . threads

integer

. . extra

string

. . extra-sort

string

. bwamem2

yes

. . threads

integer

. . extra

string

. . extra-sort

string

. samtools

yes

. . view

string

. bamutil

. . extra

string

. picard

yes

. . MarkDuplicates

string

yes

. . CollectMultipleMetrics

yes

. . . AlignmentSummaryMetrics

boolean

. . . BaseDistributionByCycle

boolean

. . . GcBiasMetrics

boolean

. . . InsertSizeMetrics

boolean

. . . QualityByCycleMetrics

boolean

. . . QualityScoreDistributionMetrics

boolean

. . . QualityYieldMetrics

boolean

. . . CollectAlignmentSummaryMetrics

boolean

. . . CollectBaseDistributionByCycle

boolean

. . . CollectGcBiasMetrics

boolean

. . . CollectInsertSizeMetrics

boolean

. . . CollectQualityYieldMetrics

boolean

. . . MeanQualityByCycle

boolean

. . . QualityScoreDistribution

boolean

. . . CollectSequencingArtifactMetrics

boolean

. . . RnaSeqMetrics

boolean

. . CollectMultipleMetrics-extra

string

yes

. dedup

yes

. . extra

string

. bcftools

yes

. . mpileup

string

. . call

string

. . threads

integer

. . mode

string

. . stats

string

. . stats-plot

string

. freebayes

yes

. . extra

string

. . chunksize

integer

. . threads

integer

. . compress-threads

integer

. gatk

yes

. . BaseRecalibrator

string

. . HaplotypeCaller-extra

string

. . CombineGVCFs-extra

string

yes

. . GenotypeGVCFs-extra

string

yes

. . HaplotypeCaller-java-opts

string

. . CombineGVCFs-java-opts

string

. . GenotypeGVCFs-java-opts

string

. . HaplotypeCaller-threads

integer

. gatk-variantfiltration

yes

. . SNP

string

yes

. . INDEL

string

yes

. . extra

string

yes

. gatk-vqsr

yes

. . resources

[‘array’, ‘object’]

. . resource-files

[‘array’, ‘object’]

. . annotation

[‘array’, ‘object’]

. . variantrecalibrator-extra-SNP

string

. . variantrecalibrator-extra-INDEL

string

. . variantrecalibrator-java-opts

string

. . applyvqsr-extra-SNP

string

. . applyvqsr-extra-INDEL

string

. . applyvqsr-java-opts

string

. bcftools-filter

yes

. . SNP

string

yes

. . INDEL

string

yes

. . extra

string

yes

. fastqc

yes

. . input

string

. . extra

string

. qualimap

yes

. . bams

string

. . extra

string

. . threads

integer

. snpeff

yes

. . name

string

. . download-dir

string

. . custom-db-dir

string

. . extra

string

. mapdamage

yes

. . extra

string

. damageprofiler

yes

. . extra

string

. seqkit

yes

. . extra

string

. multiqc

yes

. . extra

string

Linting and formatting

Linting results
1Using workflow specific profile workflow/profiles/default for setting default command line arguments.
2AttributeError in file "/tmp/tmp3ffvxqbq/workflow/rules/initialize.smk", line 24:
3'Logger' object has no attribute 'mode'
4  File "/tmp/tmp3ffvxqbq/workflow/rules/initialize.smk", line 24, in <module>
Formatting results
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69(see https://www.python.org/dev/peps/pep-0008/#id30)
70[DEBUG] In file "/tmp/tmp3ffvxqbq/workflow/rules/frequency.smk":  Formatted content is different from original
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76[DEBUG] In file "/tmp/tmp3ffvxqbq/workflow/rules/mapping.smk":  Formatted content is different from original
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81[INFO] 5 file(s) would be changed 😬
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84snakefmt version: 0.11.5