Brad Chapman chapmanb

## met_cnvs.txt
2-584759 no MET
2-584751 MET (FISH and ddPCR)
2-584699 MET (FISH and ddPCR)

## bcbio_vm_install.sh
#!/bin/bash
set -eu -o pipefail

export TARGETDIR=`pwd`/anaconda
export BINDIR=`pwd`
wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
bash Miniconda2-latest-Linux-x86_64.sh -b -p $TARGETDIR
$TARGETDIR/bin/conda install --yes -c conda-forge -c bioconda bcbio-nextgen
$TARGETDIR/bin/conda install --yes -c conda-forge -c bioconda bcbio-nextgen-vm
mkdir -p $BINDIR/bin

## Seracare_CNV_control_a-normalized.cnr
chromosome	start	end	gene	log2	depth	weight
chr1	500	1094854	Antitarget	-0.447257	0.03	0.708181
chr1	1094854	2189208	Antitarget	0.193	0.08	0.869498
chr1	2189708	2189781	FAAP20	0.166003	58.58	0.0757517
chr1	2191894	2192048	FAAP20	0.684696	184.21	0.125722
chr1	2192048	2192202	FAAP20	-0.549982	263.06	0.0954321
chr1	2192202	2192357	FAAP20	0.391232	247.57	0.125377
chr1	2192357	2192511	FAAP20	0.949453	287.09	0.1122
chr1	2192511	2192666	FAAP20	0.496266	206.08	0.113593
chr1	2192666	2192820	FAAP20	0.265958	58.87	0.0857653

## bcbio-cromwell-gcp.conf
include required(classpath("application"))

system {
  workflow-restart = true
}
call-caching {
  enabled = true
}
load-control {
  # Avoid watching memory, since the load-controller stops jobs on local runs

## sacCer3.chrom.sizes
chrI	230218
chrII	813184
chrIII	316620
chrIV	1531933
chrV	576874
chrVI	270161
chrVII	1090940
chrVIII	562643
chrIX	439888
chrX	745751

## tcga_capture.R
#!/usr/bin/env Rscript

library(GenomicDataCommons)
library(dplyr)

manifest = GenomicDataCommons::files() %>%
  GenomicDataCommons::filter(~ cases.project.project_id == "TCGA-LUAD" &
           experimental_strategy == "WXS" &
           data_format == "BAM") %>%
  GenomicDataCommons::manifest()

## bcbio-cromwell-http.conf

include required(classpath("application"))

system {
  workflow-restart = true
}
call-caching {
  enabled = true
}
load-control {

## extract_umis.py
from __future__ import print_function
import collections
import gzip
import sys

from Bio.SeqIO.QualityIO import FastqGeneralIterator

nbases = 15
nreads = 1e6
toshow = 20

## main-arvados_testcwl-pack.cwl
{
    "cwlVersion": "v1.0",
    "$graph": [
        {
            "class": "Workflow",
            "hints": [],
            "inputs": [
                {
                    "id": "#main/config__algorithm__align_split_size",
                    "type": {

## CCDS_IDTxGEN_SeqCap-hg19.bed
chr1	14395	14616	.
chr1	14672	14802	.
chr1	14832	14992	.
chr1	15012	15148	.
chr1	15611	16024	.
chr1	16541	16877	.
chr1	16893	17032	.
chr1	17251	17374	.
chr1	17403	17519	.