WHops/triopull-asm

A snakemake workflow for pulling reads out of a trio of bamfiles, and making a local assembly using hifiasm.

Overview

Latest release: None, Last update: 2024-04-12

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/WHops/triopull-asm . --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.

Description of parameters in Snake.config.json

{ "interval" : "", "ref_fa" : "", "mother_bam" : "", "father_bam" : "", "child_bam" : "" }

Interval to extract from the input bam files

interval: "chr1-5000000-6000000"

Fasta file to which the de-novo assemblies will be automatically mapped

ref_fa : "/your/hg38.fa"

Paths to the (indexed!) bam files of mother, father and child of a trio

mother_bam : "/path/to/mother.bam"
father_bam : "/path/to/father.bam"
child_bam : "/path/to/child.bam"

Linting and formatting

Linting results

 1Starting the Triopull pipeline to create local assemblies and align those to the specified referenceLints for snakefile /tmp/tmppfuxve2o/workflow/Snakefile:
 2    * Mixed rules and functions in same snakefile.:
 3      Small one-liner functions used only once should be defined as lambda
 4      expressions. Other functions should be collected in a common module, e.g.
 5      'rules/common.smk'. This makes the workflow steps more readable.
 6      Also see:
 7      https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
 8
 9Lints for rule assemble_child_trio (line 82, /tmp/tmppfuxve2o/workflow/Snakefile):
10    * Param prefix is a prefix of input or output file but hardcoded:
11      If this is meant to represent a file path prefix, it will fail when
12      running workflow in environments without a shared filesystem. Instead,
13      provide a function that infers the appropriate prefix from the input or
14      output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
15      Also see:
16      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
17      https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
18
19Lints for rule gzip_vcf (line 307, /tmp/tmppfuxve2o/workflow/Snakefile):
20    * No log directive defined:
21      Without a log directive, all output will be printed to the terminal. In
22      distributed environments, this means that errors are harder to discover.
23      In local environments, output of concurrent jobs will be mixed and become
24      unreadable.
25      Also see:
26      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
27
28Lints for rule index_vcf_gz (line 338, /tmp/tmppfuxve2o/workflow/Snakefile):
29    * No log directive defined:
30      Without a log directive, all output will be printed to the terminal. In
31      distributed environments, this means that errors are harder to discover.
32      In local environments, output of concurrent jobs will be mixed and become
33      unreadable.
34      Also see:
35      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
36
37Lints for rule index_bam (line 369, /tmp/tmppfuxve2o/workflow/Snakefile):
38    * No log directive defined:
39      Without a log directive, all output will be printed to the terminal. In
40      distributed environments, this means that errors are harder to discover.
41      In local environments, output of concurrent jobs will be mixed and become
42      unreadable.
43      Also see:
44      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files

Formatting results

1[DEBUG] 
2[DEBUG] In file "/tmp/tmppfuxve2o/workflow/Snakefile":  Formatted content is different from original
3[INFO] 1 file(s) would be changed 😬
4
5snakefmt version: 0.10.0