4_Notebook_to_Workflow.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {
    "kernel": "SoS"
   },
   "source": [
    "## Creation of a SoS workflow from interactive analysis"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "kernel": "SoS"
   },
   "source": [
    "## Basic Syntax"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "kernel": "SoS"
   },
   "source": [
    "### Script format of function calls"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "kernel": "SoS"
   },
   "outputs": [],
   "source": [
    "res_file = 'test.pdf'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "kernel": "SoS"
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "null device \n",
      "          1 \n"
     ]
    }
   ],
   "source": [
    "R(f'''\n",
    "pdf('{res_file}')\n",
    "plot(0, 0)\n",
    "dev.off()\n",
    "''', workdir='result')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "kernel": "SoS"
   },
   "source": [
    "is equivalent to"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "kernel": "SoS"
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "null device \n",
      "          1 \n"
     ]
    }
   ],
   "source": [
    "R: expand=True, workdir='result'\n",
    "    pdf('{res_file}')\n",
    "    plot(0, 0)\n",
    "    dev.off()  "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "kernel": "SoS"
   },
   "source": [
    "Or with different sigil"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "kernel": "SoS"
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "null device \n",
      "          1 \n"
     ]
    }
   ],
   "source": [
    "R: expand='${ }', workdir='result'\n",
    "    pdf('${res_file}')\n",
    "    plot(0, 0)\n",
    "    dev.off()  "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "kernel": "SoS"
   },
   "outputs": [],
   "source": [
    "[RNASeq_20 (QC)]\n",
    "\n",
    "parameter: fastq_files = list\n",
    "\n",
    "input:   fastq_files, group_by=1\n",
    "depends: executable('fastqc')\n",
    "output:  f'{_input:bn}_fastqc_html'\n",
    "\n",
    "print(f'Processing {_input}')\n",
    "\n",
    "task: walltime='30m'\n",
    "\n",
    "sh: expand=True\n",
    "    fastqc {_input}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "kernel": "SoS"
   },
   "source": [
    "### Interactive data analysis"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "kernel": "SoS"
   },
   "source": [
    "Interactive data analysis can be performed in cells with different kernels as follows. Because SoS is an extension to Python 3, you can use arbitrary Python statements in SoS cells."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "kernel": "SoS"
   },
   "outputs": [],
   "source": [
    "excel_file = 'data/DEG.xlsx'\n",
    "csv_file = 'DEG.csv'\n",
    "figure_file = 'output.pdf'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "kernel": "Bash"
   },
   "outputs": [],
   "source": [
    "%expand\n",
    "xlsx2csv {excel_file} > {csv_file}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "kernel": "R"
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<strong>pdf:</strong> 2"
      ],
      "text/latex": [
       "\\textbf{pdf:} 2"
      ],
      "text/markdown": [
       "**pdf:** 2"
      ],
      "text/plain": [
       "pdf \n",
       "  2 "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%expand\n",
    "data <- read.csv('{csv_file}')\n",
    "pdf('{figure_file}')\n",
    "plot(data$log2FoldChange, data$stat)\n",
    "dev.off()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "kernel": "R"
   },
   "source": [
    "### Convert to SoS actions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "kernel": "SoS"
   },
   "outputs": [],
   "source": [
    "excel_file = 'data/DEG.xlsx'\n",
    "csv_file = 'DEG.csv'\n",
    "figure_file = 'output.pdf'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "kernel": "SoS"
   },
   "outputs": [],
   "source": [
    "sh: expand=True\n",
    "  xlsx2csv {excel_file} > {csv_file}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "kernel": "SoS"
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "null device \n",
      "          1 \n"
     ]
    }
   ],
   "source": [
    "R: expand=True\n",
    "  data <- read.csv('{csv_file}')\n",
    "  pdf('{figure_file}')\n",
    "  plot(data$log2FoldChange, data$stat)\n",
    "  dev.off()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "kernel": "R"
   },
   "source": [
    "### Conversion to a SoS Workflow"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "kernel": "R"
   },
   "source": [
    "SoS workflows within a SoS Notebook are defined by sections marked by section headers (`[name: option]`). A `[global]` section should be used for definitions that will be used by all steps.\n",
    "\n",
    "You also need to convert scripts to SoS actions so that they can be executed as **complete** scripts. Remember also to change the cell type from subkernel to SoS."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "kernel": "SoS"
   },
   "outputs": [],
   "source": [
    "[global]\n",
    "excel_file = 'data/DEG.xlsx'\n",
    "csv_file = 'DEG.csv'\n",
    "figure_file = 'output.pdf'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "kernel": "SoS"
   },
   "outputs": [],
   "source": [
    "[plot_1 (convert)]\n",
    "sh: expand=True\n",
    "    xlsx2csv {excel_file} > {csv_file}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "kernel": "SoS"
   },
   "outputs": [],
   "source": [
    "[plot_2 (plot)]\n",
    "R: expand=True\n",
    "    data <- read.csv('{csv_file}')\n",
    "    pdf('{figure_file}')\n",
    "    plot(data$log2FoldChange, data$stat)\n",
    "    dev.off()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "kernel": "SoS"
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "null device \n",
      "          1 \n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div class=\"sos_logging sos_info\">INFO: Workflow plot (ID=e9a443b49c71e268) is executed successfully with 2 completed steps.</div>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%sosrun plot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "kernel": "SoS"
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<textarea id=\"preview_wf_46878\">#!/usr/bin/env sos-runner\n",
       "#fileformat=SOS1.0\n",
       "\n",
       "[RNASeq_20 (QC)]\n",
       "\n",
       "parameter: fastq_files = list\n",
       "\n",
       "input:   fastq_files, group_by=1\n",
       "depends: executable('fastqc')\n",
       "output:  f'{_input:bn}_fastqc_html'\n",
       "\n",
       "print(f'Processing {_input}')\n",
       "\n",
       "task: walltime='30m'\n",
       "\n",
       "sh: expand=True\n",
       "    fastqc {_input}\n",
       "\n",
       "[global]\n",
       "excel_file = 'data/DEG.xlsx'\n",
       "csv_file = 'DEG.csv'\n",
       "figure_file = 'output.pdf'\n",
       "\n",
       "[plot_1 (convert)]\n",
       "sh: expand=True\n",
       "    xlsx2csv {excel_file} > {csv_file}\n",
       "\n",
       "[plot_2 (plot)]\n",
       "R: expand=True\n",
       "    data <- read.csv('{csv_file}')\n",
       "    pdf('{figure_file}')\n",
       "    plot(data$log2FoldChange, data$stat)\n",
       "    dev.off()\n",
       "\n",
       "</textarea>"
      ],
      "text/plain": [
       "#!/usr/bin/env sos-runner\n",
       "#fileformat=SOS1.0\n",
       "\n",
       "[RNASeq_20 (QC)]\n",
       "\n",
       "parameter: fastq_files = list\n",
       "\n",
       "input:   fastq_files, group_by=1\n",
       "depends: executable('fastqc')\n",
       "output:  f'{_input:bn}_fastqc_html'\n",
       "\n",
       "print(f'Processing {_input}')\n",
       "\n",
       "task: walltime='30m'\n",
       "\n",
       "sh: expand=True\n",
       "    fastqc {_input}\n",
       "\n",
       "[global]\n",
       "excel_file = 'data/DEG.xlsx'\n",
       "csv_file = 'DEG.csv'\n",
       "figure_file = 'output.pdf'\n",
       "\n",
       "[plot_1 (convert)]\n",
       "sh: expand=True\n",
       "    xlsx2csv {excel_file} > {csv_file}\n",
       "\n",
       "[plot_2 (plot)]\n",
       "R: expand=True\n",
       "    data <- read.csv('{csv_file}')\n",
       "    pdf('{figure_file}')\n",
       "    plot(data$log2FoldChange, data$stat)\n",
       "    dev.off()\n",
       "\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%preview --workflow"
   ]
  }
 ],
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