{ "cells": [ { "cell_type": "markdown", "metadata": { "kernel": "SoS" }, "source": [ "## Workflow features" ] }, { "cell_type": "markdown", "metadata": { "kernel": "SoS" }, "source": [ "## Parameters" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "kernel": "SoS" }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "null device \n", " 1 \n" ] } ], "source": [ "%run --excel-file data/DEG.xlsx\n", "\n", "[global]\n", "parameter: excel_file = path\n", "parameter: figure_file = 'output.pdf'\n", "\n", "csv_file = excel_file.with_suffix('.csv')\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" ] }, { "cell_type": "markdown", "metadata": { "kernel": "SoS" }, "source": [ "### Signature" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "kernel": "SoS" }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "null device \n", " 1 \n" ] } ], "source": [ "%run --excel-file data/DEG.xlsx\n", "\n", "[global]\n", "parameter: excel_file = path\n", "parameter: figure_file = 'output.pdf'\n", "\n", "csv_file = excel_file.with_suffix('.csv')\n", "\n", "[plot_1 (convert)]\n", "input: excel_file\n", "output: csv_file\n", "sh: expand=True\n", " xlsx2csv {_input} > {_output}\n", " \n", "[plot_2 (plot)]\n", "output: figure_file\n", "R: expand=True\n", " data <- read.csv('{_input}')\n", " pdf('{_output}')\n", " plot(data$log2FoldChange, data$stat)\n", " dev.off()\n" ] }, { "cell_type": "markdown", "metadata": { "kernel": "SoS" }, "source": [ "### Process-oriented vs Outcome oriented workflows" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "kernel": "SoS", "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "null device \n", " 1 \n" ] } ], "source": [ "%run\n", "\n", "[plot_1 (convert)]\n", "input: 'data/DEG.xlsx'\n", "output: 'DEG.csv'\n", "sh: expand=True\n", " xlsx2csv {_input} > {_output}\n", " \n", "[plot_2 (plot)]\n", "input: 'DEG.csv'\n", "output: 'DEG.pdf'\n", "R: expand=True\n", " data <- read.csv('{_input}')\n", " pdf('{_output}')\n", " plot(data$log2FoldChange, data$stat)\n", " dev.off()" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "kernel": "SoS" }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "null device \n", " 1 \n" ] } ], "source": [ "!rm -f data/DEG.csv DEG.pdf\n", "%run -t DEG.pdf\n", "\n", "[convert: provides='{filename}.csv']\n", "input: f'{filename}.xlsx'\n", "sh: expand=True\n", " xlsx2csv {_input} > {_output}\n", " \n", "[plot]\n", "input: 'data/DEG.csv'\n", "output: 'DEG.pdf'\n", "R: expand=True\n", " data <- read.csv('{_input}')\n", " pdf('{_output}')\n", " plot(data$log2FoldChange, data$stat)\n", " dev.off()\n" ] }, { "cell_type": "markdown", "metadata": { "kernel": "SoS" }, "source": [ "### DAG" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "kernel": "SoS" }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "rm: hg19.fa: No such file or directory\n", "rm: dbsnp.vcf: No such file or directory\n" ] } ], "source": [ "!rm hg19.fa dbsnp.vcf" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "kernel": "SoS" }, "outputs": [ { "data": { "text/html": [ "