Executing NeatSeq-Flow

Author: Menachem Sklarz

Step 1: Workflow script generation

Using the GUI

To execute the script generator, go to the Run tab and click on Generate scripts.

If you see the following lines in the Terminal box, then the scripts were generated successfully:

Reading files...
Preparing objects...
Creating directory structure...
Making step instances...
Building scripts...
Making workflow plots...
Writing JSON files...
Finished successfully....

Using the command line


  1. Activate the NeatSeq_Flow conda environment:

    source activate NeatSeq_Flow
  2. Execute the following command to tell NeatSeq-Flow where the base conda installation is located:

    export CONDA_BASE=$(conda info --root)
  3. Run NeatSeq_Flow command-line version:

    neatseq_flow.py \
       --sample_file sample_data.nsfs \
       --param_file parameters.yaml \
       --message "My NeatSeq-Flow WF using conda"

Without CONDA

Executing NeatSeq-Flow’s script generator is done as follows (make sure python and neatseq_flow.py are in your search path):

python neatseq_flow.py   \
    -s sample_file.nsfs  \
    -p param_file.nsfp   \
    -m "message"         \
    -d /path/to/workflow/directory

If you get Finihed successfully... then the scripts were generated successfully.


  • NeatSeq-Flow does not require installation. If you have a local copy, append the full path to neatseq_flow.py.
  • It is not compulsory to pass a message via -m but it is highly recommended for documentation and reproducibility.
  • if -d is omitted, the current directory will be used as the workflow location.

Step 2: Executing the workflow

Using the GUI

To run the full workflow, click on Run scripts in the Run tab.


It is not possible to execute individual steps or samples with the GUI.

Using the command line

The workflow can be executed fully automatically; on a step-by-step basis or for individual samples separately.

  1. Automatic execution

    Execute the following command within the workflow directory:

    bash scripts/00.workflow.commands.sh

    The scripts/00.workflow.commands.sh script runs all the steps at once, leaving flow control entirely to the cluster job manager.

  2. Step-wise execution

    Each line in scripts/00.workflow.commands.sh calls a step-wise script in scripts/, e.g. scripts/01.Import_merge1.sh, which contains a list of qsub commands executing the individual scripts on each sample.

    The following command will execute only the merge1 step:

    qsub scripts/01.Import_merge1.sh
  3. Sample-wise execution

    The individual sample-level scripts are stored in folders within scripts/. e.g all merge1 scripts are stored in scripts/01.Import_merge1/. To execute the step only for a specific sample, execute the relevant script from within the individual script folder.