[7] Updated ATAC pipeline

The ATAC pipeline has been updated.

pipelines/wiedemann_atac_pipeline/container/fastqc_initial/run_fastqc.py

@@ -15,7 +15,7 @@ options = ""
 
 with suppress(Exception):
     adapters = MOUNT_PATHS["globals"]["ADAPTERS"]
-    options += f" --adapters {adapters}/adapters.txt"
+    options += f" --adapters {adapters}/qc_adapters.txt"
 
 kmers = os.environ.get("KMERS")
 if kmers is not None:

pipelines/wiedemann_atac_pipeline/container/fastqc_trimming/run_fastqc.py

@@ -16,7 +16,7 @@ options = ""
 
 with suppress(Exception):
     adapters = MOUNT_PATHS["globals"]["ADAPTERS"]
-    options += f" --adapters {adapters}/adapters.txt"
+    options += f" --adapters {adapters}/qc_adapters.txt"
 
 kmers = os.environ.get("KMERS")
 if kmers is not None:

pipelines/wiedemann_atac_pipeline/container/trimmomatic/run_trimming.py

@@ -2,6 +2,8 @@
 """This module runs the trimming process."""
 
 import json
+import math
+import multiprocessing
 import os
 import sys
 
@@ -13,6 +15,11 @@ INPUT_FOLDER = MOUNT_PATHS["input"] + "/"
 
 # If a specific environment variable is set, appends the respective option.
 options = ""
+
+threads = math.floor(multiprocessing.cpu_count() * 0.8)
+if threads > 0:
+    options += f" -threads {threads}"
+
 phred = os.environ.get("PHRED")
 if phred is not None:
     if phred == "PHRED33":

pipelines/wiedemann_atac_pipeline/pipeline.json

@@ -1,7 +1,7 @@
 {
   "id": "wiedemann_atac_paired_end",
   "name": "Wiedemann ATAC paired end pipeline",
-  "description": "<p>This pipeline processes paired end ATAC data. The input is expected as gzipped FASTQ files (.fq.gz / .fastq.gz) and might be organised in sub-folders.</p>",
+  "description": "<p>This pipeline processes paired end ATAC data.</p><p><b>Input specifications</b><br />The input is expected as gzipped FASTQ files (<var>.fq.gz</var> / <var>.fastq.gz</var>) and might be organised in sub-folders. Paired reads must always reside in the same folder and end with <var>_1</var> or <var>_2</var> respectively.</p><p><b>System requirements</b><br />64 GB of RAM are recommended for pipeline execution.</p>",
   "steps": [
     {
       "id": "qc_initial",
@@ -13,7 +13,7 @@
         {
           "id": "ADAPTERS",
           "name": "Adapter sequences",
-          "description": "A custom list of sequencing adapters. The global data repository must contain a file called <var>adapters.txt</var> at its root.",
+          "description": "A custom list of sequencing adapters. The global data repository must contain a file called <var>qc_adapters.txt</var> at its root.",
           "category": {
             "tag": "Global"
           }
@@ -74,7 +74,7 @@
         {
           "id": "ADAPTERS",
           "name": "Adapter sequences",
-          "description": "A custom list of sequencing adapters. The global data repository must contain a file called <var>adapters.txt</var> at its root.",
+          "description": "A custom list of sequencing adapters. The global data repository must contain a file called <var>qc_adapters.txt</var> at its root.",
           "category": {
             "tag": "Global"
           }