notebook/03_nxf_execution_conda.ipynb

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 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Run pipeline with nextflow and conda\n",
    "\n",
    "You need to install Conda and Nextflow before running this notebook following the corresponding instructions [here](https://docs.conda.io/projects/conda/en/latest/user-guide/install/) and [here](https://www.nextflow.io/docs/latest/getstarted.html#installation).\n",
    "\n",
    "> **_Note:_** Assumes you launched the notebook from `your_path/BovReg-Reproducibility/notebook/`\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Commands to change to the base directory of the repository\n",
    "import os, shutil\n",
    "pwd = os.getcwd()\n",
    "pipeline_folder = pwd + \"/../\" + \"rnaseq-nf\" \n",
    "\n",
    "os.chdir(pipeline_folder)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!nextflow run main.nf -profile conda"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Calling firefox to display multiQC report "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!firefox results_multiqc/multiqc_report.html"
   ]
  }
 ],
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