sneuensc/mapache
mapping pipeline for ancient DNA
Overview
Topics: adna ancient-dna genomics mapping mapper pipeline workflow snakemake fastq bam
Latest release: v0.3.0, Last update: 2024-10-28
Linting: linting: failed, Formatting:formatting: failed
Deployment
Step 1: Install Snakemake and Snakedeploy
Snakemake and Snakedeploy are best installed via the Mamba package manager (a drop-in replacement for conda). If you have neither Conda nor Mamba, it is recommended to install Miniforge. More details regarding Mamba can be found here.
When using Mamba, run
mamba create -c conda-forge -c bioconda --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
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/sneuensc/mapache . --tag v0.3.0
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
.
To configure this workflow, modify config/config.yaml
according to your needs.
To run mapache
at least the following two parameters have to be set in the file config/config.yaml
:
- a reference genome (e.g., hg19 human reference genome):
genome:
hg19: ## prefix for the reference genome (free to choose)
fasta: path_to_reference/foo.fasta ## file location
- the path to the sample file
samples.tsv
:
sample_file: config/samples.tsv
The sample file samples.tsv
lists all fastq files
and their relationship to library
and sample
in a tab seperated format. For single-end libraries the format is:
SM | LB | Data | ID |
---|---|---|---|
ind1 | lib1_lb | lib1_R1_001.fastq.gz | lib1_R1_001_fq |
ind1 | lib1_lb | lib1_R1_002.fastq.gz | lib1_R1_002_fq |
ind1 | lib2_lb | lib2_R1_001.fastq.gz | lib2_R1_001_fq |
ind1 | lib2_lb | lib2_R1_002.fastq.gz | lib2_R1_002_fq |
ind2 | lib3_lb | lib3_R1_001.fastq.gz | lib3_R1_001_fq |
ind2 | lib3_lb | lib3_R1_002.fastq.gz | lib3_R1_002_fq |
where
- SM: sample name
- LB: library name
- ID: uniq identifier for the fastq file (row)
-
Data: path to the
fastq file
For more details, please read the Wiki. The code is available on GitHub.
After configuering the files config/config.yaml
and the samples.tsv
you can run mapache
using the command
snakemake -j1
Linting and formatting
Linting results
/tmp/tmpsjfdl1ld/sneuensc-mapache-54c773d/workflow/scripts/utils.py:357: SyntaxWarning: invalid escape sequence '\s'
delim = get_param(["delim"], "\s+")
/tmp/tmpsjfdl1ld/sneuensc-mapache-54c773d/workflow/scripts/utils.py:467: SyntaxWarning: invalid escape sequence '\s'
delim = get_param(["delim"], "\s+")
ERROR: Reference genome config[hg19] does not exist (/work/FAC/FBM/DBC/amalaspi/popgen/shared_resources/reference_human/hs.build37.1/hs.build37.1.fa)!
grep: /work/FAC/FBM/DBC/amalaspi/popgen/shared_resources/reference_human/hs.build37.1/hs.build37.1.fa: No such file or directory
ERROR: Fastq file '/work/FAC/FBM/DBC/amalaspi/popgen/cegamorim/Andes/DATA/fastq_LINDO_POPOVIC/ERR4880182_1.fastq.gz' does not exist!
Formatting results
[DEBUG]
<unknown>:1: SyntaxWarning: invalid escape sequence '\*'
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[DEBUG] In file "/tmp/tmpsjfdl1ld/sneuensc-mapache-54c773d/workflow/Snakefile": Formatted content is different from original
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[DEBUG] In file "/tmp/tmpsjfdl1ld/sneuensc-mapache-54c773d/workflow/rules/fastq.smk": Formatted content is different from original
[DEBUG]
[DEBUG]
[DEBUG]
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[DEBUG] In file "/tmp/tmpsjfdl1ld/sneuensc-mapache-54c773d/workflow/rules/stats.smk": Formatted content is different from original
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[DEBUG] In file "/tmp/tmpsjfdl1ld/sneuensc-mapache-54c773d/workflow/rules/imputation_glimpse.smk": Formatted content is different from original
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[DEBUG] In file "/tmp/tmpsjfdl1ld/sneuensc-mapache-54c773d/workflow/rules/common.smk": Formatted content is different from original
[INFO] 5 file(s) would be changed 😬
[INFO] 4 file(s) would be left unchanged 🎉
snakefmt version: 0.10.2