ShiftCrypt Nextflow Pipeline

This repository contains a Nextflow pipeline that integrates the Bio2Byte tool ShiftCrypt. ShiftCrypt is used for the prediction of NMR chemical shifts using a variety of atom sets. This pipeline facilitates the execution of ShiftCrypt on NMR-related data files in either NEF or NMR-STAR format, streamlining data processing and prediction tasks.

Workflow Overview

The pipeline is designed to run the ShiftCrypt prediction tool with the following key parameters:

• Input Directory: The pipeline processes files from the specified input directory, supporting both .nef and .nmr file formats.
• Model: The user can select one of three atom set models for prediction:
  • Model 1: Full atom set.
  • Model 2: H, HA, CA, N, CB, C atoms.
  • Model 3: CA, N, H atoms.
• Original Numbering: Whether to use the original sequence numbering in the prediction (default is true).
• File Type: Specify whether the input is in NMR-STAR format (default is false for NEF files).

The core of the workflow is the PREDICT_SHIFTCRYPT module, which handles the execution of ShiftCrypt for each input file. The input files are automatically identified and processed, with results being output to a specified directory.

Pipeline Structure

params.inputDir = params.inputDir ?: "./data"
params.outputDir = params.outputDir ?: "./results"

params.model = params.model ?: "1"
params.isModelStar = params.isModelStar ?: false
params.originalNumbering = params.originalNumbering ?: true

include { PREDICT_SHIFTCRYPT } from "$projectDir/modules/bio2byte"

input_files = Channel.fromPath("${params.inputDir}/*.{nef,nmr}")
    .map { file -> tuple(file.baseName, file) }

workflow {
    main:
        PREDICT_SHIFTCRYPT(
            params.model,
            params.isModelStar,
            params.originalNumbering,
            input_files
        )
}

Running the Pipeline

Requirements

• Nextflow: The pipeline is written in Nextflow DSL2 and requires Nextflow to be installed.
• Conda: Conda environments are required to run the pipeline.

Commands

To run the ShiftCrypt pipeline from this repository, follow these steps:

1. Prepare your input data files. Place your .nef or .nmr files in the input directory, or specify a custom input directory using the --inputDir parameter.
2. Run the pipeline with Nextflow:

nextflow run nf-b2btools-shiftcrypt \
    --inputDir ./data/nef_examples \
    --outputDir ./results \
    --model 1 \
    --isModelStar false \
    --originalNumbering true

# `–inputDir`: Directory containing input files (.nef or .nmr).
# `–outputDir`: Directory to store the results.
# `–model`: Choose from model 1, 2, or 3 based on atom set.
# `–isModelStar`: Set to true if using NMR-STAR files, otherwise leave as false for NEF files.
# `–originalNumbering`: Use true to retain original sequence numbering.

3. Monitor the pipeline execution through the console output or view logs in the working directory.

Output

The pipeline will output the ShiftCrypt prediction results into the directory specified by the --outputDir parameter. The results for each input file will be stored in JSON format.

License

TBD