Commit 0d2a8c03 authored by van den Berg's avatar van den Berg
Browse files

Rename libraries in config to read_groups

The pipeline currently does not support different libraries per sample,
only different read groups.
parent b89b3b6e
Pipeline #3671 passed with stages
in 29 minutes and 24 seconds
......@@ -92,8 +92,8 @@ readgroups in fastq format. They must be compressed with either `gzip` or
`bgzip`.
The configuration must be passed to the pipeline through a configuration file.
This is a json file listing the samples and their associated readgroups/
libraries, as well as the other settings to be used.
This is a json file listing the samples and their associated readgroups
as well as the other settings to be used.
An example config json can be found [here](config/example.json), and a
json schema describing the configuration file can be found [here](config/schema.json).
This json schema can also be used to validate your configuration file.
......
......@@ -76,23 +76,23 @@ containers = {
def get_forward(wildcards):
""" Get the forward fastq file from the config """
return (
config["samples"][wildcards.sample]["libraries"]
config["samples"][wildcards.sample]["read_groups"]
[wildcards.read_group]["R1"]
)
def get_reverse(wildcards):
""" Get the reverse fastq file from the config """
return (
config["samples"][wildcards.sample]["libraries"]
config["samples"][wildcards.sample]["read_groups"]
[wildcards.read_group]["R2"]
)
def get_readgroup(wildcards):
return config["samples"][wildcards.sample]["libraries"]
return config["samples"][wildcards.sample]["read_groups"]
def get_readgroup_per_sample():
for sample in config["samples"]:
for rg in config["samples"][sample]["libraries"]:
for rg in config["samples"][sample]["read_groups"]:
yield rg, sample
......
{
"samples": {
"sample_01": {
"libraries": {
"read_groups": {
"lib_l1": {
"R1": "1.fq.gz",
"R2": "2.fq.gz"
......@@ -13,7 +13,7 @@
}
},
"sample_02": {
"libraries": {
"read_groups": {
"lib_l1": {
"R1": "3.1.fq.gz",
"R2": "3.2.fq.gz"
......
......@@ -20,9 +20,9 @@
"additionalProperties": {
"description": "sample object",
"type": "object",
"required": ["libraries"],
"required": ["read_groups"],
"properties": {
"libraries": {
"read_groups": {
"type": "object",
"additionalProperties": {
"description": "library",
......
{
"samples": {
"micro": {
"libraries": {
"read_groups": {
"lib_01": {
"R1": "tests/data/fastq/micro_R1.fq.gz",
"R2": "tests/data/fastq/micro_R2.fq.gz"
......
{
"samples": {
"micro": {
"libraries": {
"read_groups": {
"lib_01": {
"R1": "tests/data/fastq/micro_R1.fq.gz",
"R2": "tests/data/fastq/micro_R2.fq.gz"
......
{
"samples": {
"micro": {
"libraries": {
"read_groups": {
"lib_01": {
"R1": "tests/data/fastq/micro_R1.fq.gz",
"R2": "tests/data/fastq/micro_R2.fq.gz"
......
{
"samples": {
"micro": {
"libraries": {
"read_groups": {
"lib_01": {
"R1": "tests/data/fastq/micro_R1.fq.gz",
"R2": "tests/data/fastq/micro_R2.fq.gz"
......
{
"samples": {
"micro": {
"libraries": {
"read_groups": {
"lib_01": {
"R1": "tests/data/fastq/micro_R1.fq.gz",
"R2": "tests/data/fastq/micro_R2.fq.gz"
......
{
"samples": {
"micro": {
"libraries": {
"read_groups": {
"lib_01": {
"R1": "tests/data/fastq/micro_R1.fq.gz",
"R2": "tests/data/fastq/micro_R2.fq.gz"
......
{
"samples": {
"micro": {
"libraries": {
"read_groups": {
"lib_01": {
"R1": "tests/data/fastq/micro_R1.fq.gz",
"R2": "tests/data/fastq/micro_R2.fq.gz"
......
{
"samples": {
"micro": {
"libraries": {
"read_groups": {
"lib_01": {
"R1": "tests/data/fastq/micro_R1.fq.gz",
"R2": "tests/data/fastq/micro_R2.fq.gz"
......
{
"samples": {
"micro": {
"libraries": {
"read_groups": {
"lib_01": {
"R1": "tests/data/fastq/micro_rg1_R1.fq.gz",
"R2": "tests/data/fastq/micro_rg1_R2.fq.gz"
......
{
"samples": {
"micro1": {
"libraries": {
"read_groups": {
"lib_01": {
"R1": "tests/data/fastq/micro_rg1_R1.fq.gz",
"R2": "tests/data/fastq/micro_rg1_R2.fq.gz"
......@@ -9,7 +9,7 @@
}
},
"micro2": {
"libraries": {
"read_groups": {
"lib_02": {
"R1": "tests/data/fastq/micro_rg2_R1.fq.gz",
"R2": "tests/data/fastq/micro_rg2_R2.fq.gz"
......
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