aryazand/fastq-process-align

snakemake based pipeline for processing and mapping fastq files

Overview

Latest release: None, Last update: 2026-04-08

Share link: https://snakemake.github.io/snakemake-workflow-catalog?wf=aryazand/fastq-process-align

Quality control: linting: failed formatting: failed

Wrappers: bio/bowtie2/align bio/bowtie2/build bio/bwa-mem2/index bio/bwa-mem2/mem bio/deeptools/bamcoverage bio/fastp bio/fastqc bio/gffread bio/minimap2/aligner bio/minimap2/index bio/multiqc bio/rseqc/bam_stat bio/rseqc/infer_experiment bio/samtools/faidx bio/samtools/index bio/samtools/sort bio/samtools/view bio/star/align bio/star/index bio/trim_galore/pe

Workflow Rule Graph

This visualization of the workflow’s rule graph was automatically generated using Snakevision

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/aryazand/fastq-process-align . --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 4: Run workflow

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

To run the workflow using a combination of conda and apptainer/singularity for software deployment, use

snakemake --cores all --sdm conda apptainer

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.

Workflow overview

This workflow is a best-practice workflow for mapping of reads to reference genomes, minimalistic and simple. It will attempt to map reads to the reference using one of the included mappers, report read and experiment statistics

The workflow is built using snakemake and consists of the following steps:

Download genome reference from NCBI (ncbi tools), or use manual input (fasta, gff format)
Check quality of input read data (FastQC)
Trim adapters and apply quality filtering (fastp)
Map reads to reference genome using:
1. (Bowtie2)[http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml] or
2. (BWA-MEM2)[https://github.com/bwa-mem2/bwa-mem2] or
3. (STAR)[https://github.com/alexdobin/STAR]
4. (minimap2)[https://github.com/lh3/minimap2]
Determine experiment type, get mapping stats (rseqc)
Generate bigwig or bedgaph coverage profiles (deeptools)
Collect statistics from tool output (MultiQC)

Running the workflow

Input data

The workflow requires sequencing data in *.fastq.gz format, and a reference genome to map to. The sample sheet listing read input files needs to have the following layout:

sample	description	read1	read2
sample1	strain XY	sample1_R1.fastq.gz	sample1_R2.fastq.gz
…	…	…	…

Parameters

This table lists all parameters that can be used to run the workflow.

parameter	type	details	default
samplesheet	string	path to the sample sheet in tsv format
get_genome
database	string	database to use for genome retrieval, ‘ncbi’ or ‘manual’	`ncbi`
assembly	string	Refseq ID to use for genome retrieval	`GCF_000307535.1`
fasta	string	path to a custom FASTA file (optional)
gff	string	path to a custom GFF file (optional)
gff_source_type	array	mapping of GFF source types to feature types
fastp
extra	string	additional arguments to Fastp
mapping
tool	string	mapping tool to use, one of ‘bowtie2’, ‘bwa_mem2’	`bwa_mem2`
bowtie2
index	string	additional arguments to bowtie build
extra	string	additional arguments to bowtie align
bwa_mem2
extra	string	additional arguments to bwa-mem2
sort	string	sorting tool to use	`samtools`
sort_order	string	sorting order to use	`coordinate`
sort_extra	string	additional arguments to the sorting tool
samtools_sort
extra	string	additional arguments to Samtools sort	`-m 4G`
index	object	Samtools index options
extra	string	additional arguments to Samtools index
star
index	string	additional arguments to STAR index
extra	string	additional arguments to STAR align
minimap2
index	string	additional arguments to minimap2 index
extra	string	additional arguments to minimap2 align	`-ax map-ont`
sorting	string	sorting order to use	`coordinate`
sort_extra	string	additional arguments to the sorting tool
mapping_stats
gffread
extra	string	additional arguments to GFFread
rseqc_infer_experiment
extra	string	additional arguments to RSeQC infer_experiment
rseqc_bam_stat
extra	string	additional arguments to RSeQC bam_stat
deeptools_coverage
genome_size	integer	genome size in base pairs	`1000`
extra	string	additional arguments to DeepTools bamCoverage
qc
fastqc
extra	string	additional arguments to FastQC
multiqc
extra	string	additional arguments to MultiQC

Workflow parameters

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

Parameter	Type	Description	Required
samplesheet	string	path to the sample sheet in tsv format	yes
get_genome			yes
. database	string	database to use for genome retrieval, ‘ncbi’ or ‘manual’	yes
. assembly	string	assembly version to use for genome retrieval, e.g. ‘GCF_000307535.1’	yes
. fasta	[‘string’, ‘null’]	path to a custom FASTA file (optional)
. gff	[‘string’, ‘null’]	path to a custom GFF file (optional)
. gff_source_type	array	mapping of GFF source types to feature types	yes
processing			yes
. tool	string	which tool is being used to process fastq files
. fastp
. . extra	string	additional arguments to pass to Fastp
. trim_galore
. . extra	string	additional arguments to pass to trim_galore
. umi_tools_extract
. . enabled	boolean	whether to extract UMIs with umi_tools extract
. . extra	string	additional arguments to pass to umi_tools extract
mapping			yes
. tool	string	mapping tool to use, one of ‘bowtie2’, ‘bwa_mem2’, ‘star’
. bowtie2
. . index	string	additional arguments to bowtie build
. . extra	string	additional arguments to bowtie align
. bwa_mem2
. . extra	string	additional arguments to bwa-mem2
. . sort	string	sorting tool to use, e.g. ‘samtools’
. . sort_order	string	sorting order to use
. . sort_extra	string	additional arguments to pass to the sorting tool
. star
. . index	string	additional arguments to STAR index
. . extra	string	additional arguments to STAR align
. minimap2
. . index	string	additional arguments to minimap2 index
. . extra	string	additional arguments to minimap2 align
. . sorting	string	sorting order to use
. . sort_extra	string	additional arguments to pass to the sorting tool
. samtools_sort
. . extra	string	additional arguments to pass to Samtools sort
. samtools_index
. . extra	string	additional arguments to pass to Samtools index
. umi_tools_dedup
. . enabled	boolean	whether to dedup with umi_tools dedup
. . extra	string	additional arguments to pass to umi_tools dedup
mapping_stats			yes
. gffread			yes
. . extra	string	additional arguments to pass to GFFread
. rseqc_infer_experiment			yes
. . extra	string	additional arguments to pass to RSeQC infer_experiment.py
. rseqc_bam_stat			yes
. . extra	string	additional arguments to pass to RSeQC bam_stat.py
. deeptools_coverage			yes
. . genome_size	integer	genome size in base pairs
. . extra	string	additional arguments to pass to DeepTools bamCoverage
qc			yes
. multiqc			yes
. . extra	string	additional arguments to pass to MultiQC
. fastqc			yes
. . extra	string	additional arguments to pass to FastQC

Linting and formatting

Linting results

Lints for rule add_overhang_for_circular_chromosomes (line 1, /tmp/tmphjjs0c87/workflow/rules/overhang.smk):
    * No log directive defined:
      Without a log directive, all output will be printed to the terminal. In
      distributed environments, this means that errors are harder to discover.
      In local environments, output of concurrent jobs will be mixed and become
      unreadable.
      Also see:
      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files

Lints for rule remove_overhang (line 32, /tmp/tmphjjs0c87/workflow/rules/process_bam.smk):
    * Specify a conda environment or container for each rule.:
      This way, the used software for each specific step is documented, and the
      workflow can be executed on any machine without prerequisites.
      Also see:
      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers

Formatting results

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[DEBUG] In file "/tmp/tmphjjs0c87/workflow/rules/process_bam.smk":  Formatted content is different from original
[INFO] 1 file(s) would be changed 😬
[INFO] 12 file(s) would be left unchanged 🎉

snakefmt version: 0.11.5