I’m trying to understand how workflows work in UKBiobank’s Research Analysis Platform (RAP). I wanted to create a sample workflow of saving just the head of an input dataset and saving this subsetted dataset in a directory. I’m getting an error pertaining to the ‘command’ section of my WDL script.

WDL script:

workflow save_head_workflow {
  input {
    File input_file         # Input dataset file
    Int num_rows = 5        # Number of rows to return (default is 5)
  }

  call saveHead {
    input:
      input_file = input_file,
      num_rows = num_rows
  }

  output {
    File output_file = saveHead.output_file
  }
}

task saveHead {
  input {
    File input_file         # Input dataset file
    Int num_rows            # Number of rows to extract
  }

  command {
  python save_head.py --input ${input_file} --rows ${num_rows} --output output_head.csv
  }

  output {
    File output_file = "output_head.csv"
  }

  runtime {
    docker: "python:3.9-slim"  # Lightweight Docker image with Python 3.9
  }
}

save_head.py (the python script mentioned in the command in the above section):

import pandas as pd
import argparse

def save_head(input_file, num_rows, output_file):
    """
    Reads a dataset and saves the first `num_rows` rows to the output file.

    Args:
        input_file (str): Path to the input file.
        num_rows (int): Number of rows to save.
        output_file (str): Path to the output file.
    """
    # Read the dataset
    df = pd.read_csv(input_file, sep=None, engine="python")  # Auto-detect delimiter (CSV or TSV)
    
    # Extract the head
    head_df = df.head(num_rows)
    
    # Save the head to the output file
    head_df.to_csv(output_file, index=False)
    print(f"Saved the first {num_rows} rows to {output_file}")

My json file indicating the input dataset:

{
    "return_head_workflow.input_file": "/mnt/project/Participant_table.csv",
    "return_head_workflow.num_rows": 5
}

The error that I get is somewhat like (the error passage is long but below is ultimately the error I believe:
Caused by: wdlTools.syntax.SyntaxException: section command appears 0 times, it must appear exactly once at 18:0-50:1 in /home/dnanexus/return_head.wdl

Could anyone help me understand if there was anything wrong in the script(s) and kindly rectify them? Thanks in advance!