Revert "sync"

GWAS/GWAS_QC.ipynb

@@ -2,7 +2,7 @@
  "cells": [
  {
  "cell_type": "markdown",
- "id": "signal-secretary",
+ "id": "",
  "metadata": {
  "kernel": "SoS"
  },
@@ -14,7 +14,7 @@
  },
  {
  "cell_type": "markdown",
- "id": "disturbed-colonial",
+ "id": "",
  "metadata": {
  "kernel": "SoS"
  },
@@ -30,7 +30,7 @@
  },
  {
  "cell_type": "markdown",
- "id": "liable-program",
+ "id": "",
  "metadata": {
  "kernel": "SoS"
  },
@@ -47,7 +47,7 @@
  },
  {
  "cell_type": "markdown",
- "id": "lasting-vegetation",
+ "id": "",
  "metadata": {
  "kernel": "SoS"
  },
@@ -87,7 +87,7 @@
  {
  "cell_type": "code",
  "execution_count": 1,
- "id": "continent-fetish",
+ "id": "",
  "metadata": {
  "kernel": "Bash"
  },
@@ -181,7 +181,7 @@
  {
  "cell_type": "code",
  "execution_count": null,
- "id": "complicated-optimization",
+ "id": "",
  "metadata": {
  "kernel": "SoS"
  },
@@ -209,7 +209,7 @@
  },
  {
  "cell_type": "markdown",
- "id": "chicken-architecture",
+ "id": "",
  "metadata": {
  "kernel": "SoS"
  },
@@ -222,7 +222,7 @@
  {
  "cell_type": "code",
  "execution_count": null,
- "id": "later-shark",
+ "id": "",
  "metadata": {
  "kernel": "SoS"
  },
@@ -443,7 +443,7 @@
  },
  {
  "cell_type": "markdown",
- "id": "falling-combination",
+ "id": "",
  "metadata": {
  "kernel": "SoS"
  },
@@ -458,7 +458,7 @@
  {
  "cell_type": "code",
  "execution_count": 2,
- "id": "exotic-moses",
+ "id": "",
  "metadata": {
  "kernel": "SoS"
  },
@@ -484,8 +484,6 @@
  "parameter: hwe_filter = 5e-08\n",
  "# Plink binary files\n",
  "parameter: genoFile = paths\n",
- "# Keep only snps\n",
- "parameter: snps_only = False\n",
  "\n",
  "fail_if(not (keep_samples.is_file() or keep_samples == path('.')), msg = f'Cannot find ``{keep_samples}``')\n",
  "fail_if(not (keep_variants.is_file() or keep_variants == path('.')), msg = f'Cannot find ``{keep_variants}``')\n",
@@ -497,15 +495,14 @@
  "bash: container=container_lmm, volumes=[f'{cwd}:{cwd}'], expand= \"${ }\", stderr = f'{_output:n}.stderr', stdout = f'{_output:n}.stdout'\n",
  " plink2 \\\n",
  " --bfile ${_input:n} \\\n",
- " ${('--maf %s' % maf_filter) if maf_filter > 0 else ''} \\\n",
+ " ${('--maf %s' % maf_filter) if maf_filter >= 0 else ''} \\\n",
  " ${('--max-maf %s' % maf_max_filter) if maf_max_filter > 0 else ''} \\\n",
- " ${('--geno %s' % geno_filter) if geno_filter > 0 else ''} \\\n",
- " ${('--hwe %s' % hwe_filter) if hwe_filter > 0 else ''} \\\n",
- " ${('--mind %s' % mind_filter) if mind_filter > 0 else ''} \\\n",
+ " ${('--geno %s' % geno_filter) if geno_filter >= 0 else ''} \\\n",
+ " ${('--hwe %s' % hwe_filter) if hwe_filter >= 0 else ''} \\\n",
+ " ${('--mind %s' % mind_filter) if mind_filter >= 0 else ''} \\\n",
  " ${('--keep %s' % keep_samples) if keep_samples.is_file() else \"\"} \\\n",
  " ${('--remove %s' % remove_samples) if remove_samples.is_file() else \"\"} \\\n",
  " ${('--extract %s' % keep_variants) if keep_variants.is_file() else \"\"} \\\n",
- " ${('--snps-only') if snps_only is True else \"\"} \\\n",
  " --make-bed \\\n",
  " --out ${_output:n} \\\n",
  " --threads ${numThreads} \\\n",
@@ -515,7 +512,7 @@
  {
  "cell_type": "code",
  "execution_count": 1,
- "id": "passing-minute",
+ "id": "",
  "metadata": {
  "kernel": "SoS"
  },
@@ -550,7 +547,7 @@
  {
  "cell_type": "code",
  "execution_count": null,
- "id": "demographic-medicine",
+ "id": "",
  "metadata": {
  "kernel": "SoS"
  },
@@ -566,7 +563,7 @@
  {
  "cell_type": "code",
  "execution_count": null,
- "id": "resident-motel",
+ "id": "",
  "metadata": {
  "kernel": "SoS"
  },
@@ -680,7 +677,7 @@
  "displayed": true,
  "height": 0
  },
- "version": "0.22.6"
+ "version": "0.21.21"
  }
  },
  "nbformat": 4,