From 8ddcd6781f8924fc9ee5621edd79c133c7f2f64c Mon Sep 17 00:00:00 2001
From: skchronicles <kuhnsa3@gmail.com>
Date: Wed, 3 Apr 2024 11:55:26 -0400
Subject: [PATCH] Removing quality filter option from cli

---
 mpox-seek               | 20 +++-----------------
 workflow/Snakefile      |  4 ----
 workflow/rules/trim.smk |  2 +-
 3 files changed, 4 insertions(+), 22 deletions(-)

diff --git a/mpox-seek b/mpox-seek
index 6c9fce3..7da9558 100755
--- a/mpox-seek
+++ b/mpox-seek
@@ -377,7 +377,6 @@ def parsed_arguments(name, description):
                 [--silent] [--threads THREADS] [--tmp-dir TMP_DIR] \\
                 [--resource-bundle RESOURCE_BUNDLE] [--use-conda] \\
                 [--conda-env-name CONDA_ENV_NAME] \\
-                [--quality-filter QUALITY_FILTER] \\
                 --input INPUT [INPUT ...] \\
                 --output OUTPUT
 
@@ -404,10 +403,7 @@ def parsed_arguments(name, description):
                                   Example: --output /data/$USER/output
 
         {3}{4}Analysis options:{5}
-          --quality-filter QUALITY_FILTER
-                                Filter reads on a minimum average quality score. The 
-                                default average minimum quality filter is set to 8.
-                                  Example: --quality-filter 8
+          More analysis option coming soon! 
 
         {3}{4}Orchestration options:{5}
           --mode {{slurm,local}}  
@@ -529,7 +525,7 @@ def parsed_arguments(name, description):
 
           # Step 2A.) Dry-run the pipeline
           ./{0} run --input .tests/*.fastq.gz \\
-                    --output /data/$USER/output \\
+                    --output output_01 \\
                     --mode slurm \\
                     --dry-run
 
@@ -538,7 +534,7 @@ def parsed_arguments(name, description):
           # the cluster. It is recommended running 
           # the pipeline in this mode.
           ./{0} run --input .tests/*.fastq.gz \\
-                    --output /data/$USER/output \\
+                    --output output_01 \\
                     --mode slurm
 
         {2}{3}Version:{4}
@@ -575,16 +571,6 @@ def parsed_arguments(name, description):
         help = argparse.SUPPRESS
     )
 
-    # Analysis Arguments
-    # Minimum average read quality filter 
-    subparser_run.add_argument(
-        '--quality-filter',
-        type = int,
-        required = False,
-        default = 8,
-        help = argparse.SUPPRESS
-    )
-
     # Optional Arguments
     # Add custom help message
     subparser_run.add_argument(
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 8f52150..d32fb3b 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -22,10 +22,6 @@ samples2barcodes = config['barcodes']          # Samples to demultiplex, `cat` t
 # means they need to be merged  
 barcoded_samples = [k for k in samples2barcodes if samples2barcodes[k]]
 samples = list(config['barcodes'].keys())
-# Read average quality score filter
-quality_filter = int(
-    config['options']['quality_filter']
-) # Default: 8
 
 # Determines if Conda or Singularity
 # are used for software dependencies
diff --git a/workflow/rules/trim.smk b/workflow/rules/trim.smk
index 2da9272..ca0334e 100644
--- a/workflow/rules/trim.smk
+++ b/workflow/rules/trim.smk
@@ -71,7 +71,7 @@ rule nanofilt:
         flt = join(workpath, "{name}", "fastqs", "{name}.filtered.fastq.gz"),
     params:
         rname='nanofilt',
-        qual_filt=quality_filter,
+        qual_filt=8,
     conda: depending(conda_yaml_or_named_env, use_conda)
     container: depending(config['images']['mpox-seek'], use_singularity)
     shell: