Command line interface

init

Each workflow requires a configuration and samples file to run. Running “seq2science init {workflow}” initialises a default configuration and samples file for the specific workflow. Supported workflows: alignment, scrna-seq, scatac-seq, atac-seq, rna-seq, download-fastq, chip-seq

usage: seq2science init [-h] [--dir PATH] [-f] WORKFLOW

Positional Arguments

WORKFLOW: Possible choices: alignment, scrna-seq, scatac-seq, atac-seq, rna-seq, download-fastq, chip-seq

Named Arguments

--dir

The path to the directory where to initialise the config and samples files.

Default: “.”

-f, --force

Overwrite existing samples.tsv and config.yaml silently.

Default: False

run

Run a complete workflow. This requires that a config and samples file are either present in the current directory, or passed as an argument. Supported workflows: alignment, scrna-seq, scatac-seq, atac-seq, rna-seq, download-fastq, chip-seq

usage: seq2science run [-h] [-j N] [-n] [-r] [--skip-rerun] [-k]
                       [--rerun-incomplete] [--unlock]
                       [--cleanup-metadata CLEANUP_METADATA [CLEANUP_METADATA ...]]
                       [--snakemakeOptions KEY=VAL [KEY=VAL ...]]
                       [-p PROFILE NAME] [-c FILE] [--debug]
                       WORKFLOW

Positional Arguments

WORKFLOW: Possible choices: alignment, scrna-seq, scatac-seq, atac-seq, rna-seq, download-fastq, chip-seq

Named Arguments

-j, --cores

Use at most N cores in parallel. Must be at least 2. When executing on a cluster, this number controls the maximum numberof parallel jobs.

-n, --dryrun

Do not execute anything, and display what would be done.

Default: False

-r, --reason

Print the reason for each executed rule.

Default: False

--skip-rerun

Skip the check if samples or configuration has been changed.

Default: False

-k, --keep-going

Go on with independent jobs if a job fails.

Default: False

--rerun-incomplete

Re-run all jobs the output of which is recognized as incomplete.

Default: False

--unlock

Remove a lock on the working directory.

Default: False

--cleanup-metadata

Just cleanup metadata of given list of output files (default None).

--snakemakeOptions

Extra arguments to pass along to snakemake. An example could be seq2science run alignment –cores 12 –snakemakeOptions resources={mem_gb:100} local_cores=3. Here we pass local_cores as KEY=VALUE and additional resources can even be passed along in a dictionary. Take a look at the snakemake API for a complete list of all possible options: https://snakemake-api.readthedocs.io/en/latest/api_reference/snakemake.html

-p, --profile

Use a seq2science profile. Profiles can be taken from: https://github.com/vanheeringen-lab/seq2science-profiles. Profiles are an experimental feature and might not always work as intended. Please let us know if something doesn’t work properly!

-c, --configfile

The path to the config file.

Default: “./config.yaml”

--debug

For developers “only”: prints helpful error messages to debug issues.

Default: False

clean

At the start of each workflow run, seq2science starts with installing environments for each rule. It also stores the GEO soft files of public samples in its cache. These environments can get large and it might be best to remove them when you are done with an analysis. seq2science clean will clean up these files for you.

usage: seq2science clean [-h]

explain

Explains what has/will be done for the workflow. This prints a string which can serve as a skeleton for your material & methods section. Supported workflows: alignment, scrna-seq, scatac-seq, atac-seq, rna-seq, download-fastq, chip-seq

usage: seq2science explain [-h] [--hyperref]
                           [--snakemakeOptions KEY=VAL [KEY=VAL ...]]
                           [-p PROFILE NAME] [-c FILE] [--debug]
                           WORKFLOW

Positional Arguments

WORKFLOW: Possible choices: alignment, scrna-seq, scatac-seq, atac-seq, rna-seq, download-fastq, chip-seq

Named Arguments

--hyperref

Print urls as html hyperref

Default: False

--snakemakeOptions

Extra arguments to pass along to snakemake. An example could be seq2science run alignment –cores 12 –snakemakeOptions resources={mem_gb:100} local_cores=3. Here we pass local_cores as KEY=VALUE and additional resources can even be passed along in a dictionary. Take a look at the snakemake API for a complete list of all possible options: https://snakemake-api.readthedocs.io/en/latest/api_reference/snakemake.html

-p, --profile

Use a seq2science profile. Profiles can be taken from: https://github.com/vanheeringen-lab/seq2science-profiles. Profiles are an experimental feature and might not always work as intended. Please let us know if something doesn’t work properly!

-c, --configfile

The path to the config file.

Default: “./config.yaml”

--debug

For developers “only”: prints helpful error messages to debug issues.

Default: False

docs

The docs command tries to open your browser and open the docs’ webpage, if that didn’t work it prints the url.

usage: seq2science docs [-h]