panguangze/trio_call_phase_pipeline
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Overview
Topics:
Latest release: None, Last update: 2022-09-07
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/panguangze/trio_call_phase_pipeline . --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 using a combination of conda
and apptainer
/singularity
for software deployment, use
snakemake --cores all --sdm conda apptainer
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
.
General settings
Adjust config.yaml
to configure the workflow execution. The config files samples.tsv
and joint_calling_groups.tsv
contain the following sample information:
-
samples.tsv
lists the samples as well as the read sets for each sample, with one set of reads for eachsample_id-unit
. Note thatsample_id-unit
combinations should be unique. -
joint_calling_groups.tsv
groups samples for joint calling. Note that jointly called samples will be named with the formatgroup:sample_id
in the GLnexus output and in the finalall.vcf.gz
file.
The pipeline will call all samples individually. Samples specified as belonging to the same joint calling group will be called jointly by GLnexus. To call all samples jointly, specify them as all belonging to the same joint calling group. Samples that are only called individually do not need to be specified in joint_calling_groups.tsv
.
Linting and formatting
Linting results
KeyErrorin line 10 of /tmp/tmpfnurvkko/workflow/Snakefile:
'joint_calling_groups'
File "/tmp/tmpfnurvkko/workflow/Snakefile", line 10, in <module>
Formatting results
[DEBUG]
[WARNING] In file "/tmp/tmpfnurvkko/workflow/rules/trio_calling_snp.smk": Keyword "output" at line 14 has comments under a value.
PEP8 recommends block comments appear before what they describe
(see https://www.python.org/dev/peps/pep-0008/#id30)
[DEBUG] In file "/tmp/tmpfnurvkko/workflow/rules/trio_calling_snp.smk": Formatted content is different from original
[DEBUG]
[DEBUG]
[DEBUG] In file "/tmp/tmpfnurvkko/workflow/rules/qc.smk": Formatted content is different from original
[DEBUG]
[DEBUG] In file "/tmp/tmpfnurvkko/workflow/Snakefile": Formatted content is different from original
[DEBUG]
[DEBUG] In file "/tmp/tmpfnurvkko/workflow/rules/common.smk": Formatted content is different from original
[DEBUG]
[DEBUG]
[DEBUG] In file "/tmp/tmpfnurvkko/workflow/rules/phase.smk": Formatted content is different from original
[DEBUG]
[WARNING] In file "/tmp/tmpfnurvkko/workflow/rules/trio_calling_sv.smk": Keyword "output" at line 11 has comments under a value.
PEP8 recommends block comments appear before what they describe
(see https://www.python.org/dev/peps/pep-0008/#id30)
[DEBUG] In file "/tmp/tmpfnurvkko/workflow/rules/trio_calling_sv.smk": Formatted content is different from original
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