Rename libraries in config to read_groups

The pipeline currently does not support different libraries per sample,
only different read groups.

README.md

@@ -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.

Snakefile

@@ -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
 
 

config/example.json

 {
     "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"

config/schema.json

@@ -20,9 +20,9 @@
             "additionalProperties": {
                 "description": "sample object",
                 "type": "object",
-                "required": ["libraries"],
+                "required": ["read_groups"],
                 "properties": {
-                    "libraries": {
+                    "read_groups": {
                         "type": "object",
                         "additionalProperties": {
                             "description": "library",

tests/data/config/invalid_config_fake_ref.json

 {
   "samples": {
     "micro": {
-      "libraries": {
+      "read_groups": {
         "lib_01": {
         "R1": "tests/data/fastq/micro_R1.fq.gz",
         "R2": "tests/data/fastq/micro_R2.fq.gz"

tests/data/config/invalid_config_no_ref.json

 {
   "samples": {
     "micro": {
-      "libraries": {
+      "read_groups": {
         "lib_01": {
         "R1": "tests/data/fastq/micro_R1.fq.gz",
         "R2": "tests/data/fastq/micro_R2.fq.gz"

tests/data/config/sample_config.json

 {
   "samples": {
     "micro": {
-      "libraries": {
+      "read_groups": {
         "lib_01": {
         "R1": "tests/data/fastq/micro_R1.fq.gz",
         "R2": "tests/data/fastq/micro_R2.fq.gz"

tests/data/config/sample_config_bed_all.json

 {
   "samples": {
     "micro": {
-      "libraries": {
+      "read_groups": {
         "lib_01": {
         "R1": "tests/data/fastq/micro_R1.fq.gz",
         "R2": "tests/data/fastq/micro_R2.fq.gz"

tests/data/config/sample_config_bed_target.json

 {
   "samples": {
     "micro": {
-      "libraries": {
+      "read_groups": {
         "lib_01": {
         "R1": "tests/data/fastq/micro_R1.fq.gz",
         "R2": "tests/data/fastq/micro_R2.fq.gz"

tests/data/config/sample_config_refflat.json

 {
   "samples": {
     "micro": {
-      "libraries": {
+      "read_groups": {
         "lib_01": {
         "R1": "tests/data/fastq/micro_R1.fq.gz",
         "R2": "tests/data/fastq/micro_R2.fq.gz"

tests/data/config/sample_config_scatter.json

 {
   "samples": {
     "micro": {
-      "libraries": {
+      "read_groups": {
         "lib_01": {
         "R1": "tests/data/fastq/micro_R1.fq.gz",
         "R2": "tests/data/fastq/micro_R2.fq.gz"

tests/data/config/sample_config_two_known_vcf.json

 {
   "samples": {
     "micro": {
-      "libraries": {
+      "read_groups": {
         "lib_01": {
         "R1": "tests/data/fastq/micro_R1.fq.gz",
         "R2": "tests/data/fastq/micro_R2.fq.gz"

tests/data/config/sample_config_two_readgroup.json

 {
   "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"

tests/data/config/sample_config_two_samples.json

 {
   "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"