refactor: getting rid of general thread config. now using build in re…

…sources/threads

config/example_assignment_bwa.yaml

@@ -1,6 +1,5 @@
 ---
 global: # generall configs effecting one or multiple parts
-  threads: 1
   assignments:
     split_number: 1 # number of files fastq should be split for parallelization
 assignments:

config/example_assignment_exact_lazy.yaml

@@ -1,6 +1,5 @@
 ---
 global: # generall configs effecting one or multiple parts
-  threads: 1
   assignments:
     split_number: 1 # number of files fastq should be split for parallelization
 assignments:

config/example_assignment_exact_linker.yaml

@@ -1,6 +1,5 @@
 ---
 global: # generall configs effecting one or multiple parts
-  threads: 1
   assignments:
     split_number: 1 # number of files fastq should be split for parallelization
 assignments:

config/example_config.yaml

@@ -1,6 +1,5 @@
 ---
 global: # generall configs effecting one or multiple parts
-  threads: 1
   assignments:
     split_number: 1 # number of files fastq should be split for parallelization
 assignments:
@@ -31,7 +30,7 @@ experiments:
   exampleCount:
     bc_length: 15
     umi_length: 10
-    data_folder: resources/Count_Basic/data
+    data_folder: resources/count_basic/data
     experiment_file: resources/example_experiment.csv
     demultiplex: false
     assignments:

config/example_count.yaml

@@ -0,0 +1,15 @@
+---
+experiments:
+  exampleCount:
+    bc_length: 15
+    umi_length: 10
+    data_folder: resources/count_basic/data
+    experiment_file: resources/count_basic/experiment.csv
+    demultiplex: false
+    assignments:
+      fromFile:
+        type: file
+        assignment_file: resources/count_basic/SRR10800986_barcodes_to_coords.tsv.gz
+    design_file: resources/count_basic/design.fa
+    configs:
+      default: {} # name of an example filtering config

docs/assignment_example1.rst

@@ -108,7 +108,7 @@ First we do a try run using snakemake :code:`-n` option. The MPRAsnakeflow comma
 
     cd assoc_basic
     conda activate mprasnakeflow
-    snakemake -c 1 --use-conda --snakefile /home/user/MPRAsnakeflow/workflow/Snakefile --configfile /home/user/MPRAsnakeflow/resources/assoc_basic/config.yml -n -q
+    snakemake -c 1 --sdm conda --snakefile /home/user/MPRAsnakeflow/workflow/Snakefile --configfile /home/user/MPRAsnakeflow/resources/assoc_basic/config.yml -n -q --set-threads assignment_mapping_bwa=10
 
 You should see a list of rules that will be executed. This is the summary:
 

docs/config.rst

@@ -24,8 +24,6 @@ The general settings are located in the :code:`global` section. The following se
    :start-after: start_global
    :end-before: start_assignments
 
-:threads:
-    Number of threads that are available to run a rule. Right now this is used for bwa mem in the assignment workflow. Be sure to set up the snakemake option :code:`-c` correctly when using larger number of possible threads. Default is set to 1.
 :assignments:
     Global parameters that hold for the assignment workflow.
 

resources/assoc_basic/config.yml

@@ -1,6 +1,5 @@
 ---
 global:
-  threads: 10
   assignments:
     split_number: 30
 assignments:

resources/combined_basic/config.yml

@@ -1,6 +1,5 @@
 ---
 global:
-  threads: 10
   assignments:
     split_number: 30
 assignments:

workflow/rules/assignment/mapping_bwa.smk

@@ -39,7 +39,7 @@ rule assignment_mapping_bwa:
         ),
     output:
         bam=temp("results/assignment/{assignment}/bam/merge_split{split}.mapped.bam"),
-    threads: config["global"]["threads"]
+    threads: 1
     log:
         temp("results/logs/assignment/mapping.{assignment}.{split}.log"),
     shell:
@@ -109,7 +109,7 @@ rule assignment_collect:
         ),
     output:
         "results/assignment/{assignment}/aligned_merged_reads.bam",
-    threads: config["global"]["threads"]
+    threads: 1
     log:
         temp("results/logs/assignment/collect.{assignment}.log"),
     shell:

workflow/schemas/config.schema.yaml

@@ -14,7 +14,6 @@ properties:
   global:
     type: object
     default:
-      threads: 1
       assignments:
         split_number: 1
     properties:
@@ -25,9 +24,6 @@ properties:
             type: integer
             default: 1
         additionalProperties: false
-      threads:
-        type: integer
-        default: 1
     additionalProperties: false
   # start_assignments
   assignments: