Differences

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--- scripts:qc [2025/03/12 10:13] – 37.26.174.181
+++ scripts:qc [2025/03/21 12:43] (current) – 37.26.174.181
@@ Line 92: / Line 92: @@
 echo "Running MultiQC..."
 mkdir -p "$output_dir"
-multiqc -o "$output_dir" "$input_dir/"*.fq.gz
+multiqc -o "$output_dir" "$input_dir"
 </code>
@@ Line 101: / Line 101: @@
 #SBATCH --mem=10gb
 #SBATCH --cpus-per-task=10
-#SBATCH --job-name=fastqc_multiqc_00
+#SBATCH --job-name=multiqc_00
-#SBATCH --output=log/fastqc_00%j.log  # %j will be replaced with the job ID
+#SBATCH --output=log/multiqc_00%j.log  # %j will be replaced with the job ID
 #parameters
@@ Line 114: / Line 114: @@
 You can also perform them simultaneously with one parent script:
 == Combined parent script ==
-fastqc_multiqc_00.sh
+qc_00.sh
 <code>
 #!/bin/bash
@@ Line 133: / Line 133: @@
 </code>
-You can also use the same scripts on trimmed files. Just add "_trimmed" to the inputs and outputs like this. Remember to save them in separate olders (fastqc_trimmed, multiqc_trimmed)
+You can also use the same scripts on trimmed files. Just add "_trimmed" to the inputs and outputs like this. Remember to save them in separate folders (fastqc_trimmed, multiqc_trimmed)
+fastqc_post_00.sh
 <code>
-#Input parameters
+#!/bin/bash
+#SBATCH --mem=10gb
+#SBATCH --cpus-per-task=10
+#SBATCH --job-name=fastqc_post_00
+#SBATCH --output=log/fastqc_post_00%j.log  # %j will be replaced with the job ID
+#parameters
 input=fq_trimmed
 output=fastqc_trimmed
+src/fastqc.sh $input $output
 </code>
-== Fastp ==
+multiqc_post_00.sh
-If you want to add Fastp reports to MultiQC, you can add "fq_trimmed" directory as input to MultiQC.
+<code>
+#!/bin/bash
+#SBATCH --mem=10gb
+#SBATCH --cpus-per-task=10
+#SBATCH --job-name=multiqc_post_00
+#SBATCH --output=log/multiqc_post_00%j.log  # %j will be replaced with the job ID
-In daughter script:
+#parameters
+input=fastqc_trimmed
+output=multiqc_trimmed
+src/multiqc.sh $input $output
+</code>
+=== Fastp ===
+If you want to add Fastp reports to MultiQC, you can add "fq_trimmed" directory as input to MultiQC (multiqc_fastp.sh).
+== Daughter script ==
+multiqc_fastp.sh:
 <code>
-# Rest of the code
+# SCRIPT FOR PERFORMING MultiQC
+# NOTE: Run this script from the directory where the "log" directory is located,
+#       Example: /mnt/proj/ibd/ds-06_cd-fecal/common
+#
+# PURPOSE:
+#   This script performs MultiQC.
+#
+# PARAMETERS:
+#   1: input_dir - Directory where FastQC reports are located.
+#   2: output_dir - Directory where MultiQC report will be located
+# SAMPLE USAGE:
+#   In a parent script: src/multiqc.sh <input_dir> <output_dir>
+#
+# IMPORTANT:
+#   - Run from a parent script.
+# Check if correct number of arguments are provided
+if [ "$#" -ne 2 ]; then
+    echo "Usage: $0 <input_dir> <output_dir>"
+    exit 1
+fi
 # Input parameters
-input_dir="$1"
+input_dir=$1
-input_fastp="$2"
+input_fastp=$2
-output_dir="$3"
+output_dir=$3
-# Rest of the code
+echo "Running MultiQC..."
+mkdir -p "$output_dir"
+multiqc -o "$output_dir" "$input_dir" "$input_fastp"
 </code>
-In parent script:
+== Parent ==
+multiqc_fastp_00.sh
 <code>
-# Rest of the code
+#!/bin/bash
-src/multiqc.sh $input_dir $input_fastp $output_dir
+#SBATCH --mem=10gb
+#SBATCH --cpus-per-task=10
+#SBATCH --job-name=multiqc_fastp_00
+#SBATCH --output=log/multiqc_fastp_00%j.log  # %j will be replaced with the job ID
+#parameters
+input=fastqc_trimmed
+input_fastp=fq_trimmed
+output=multiqc_trimmed
+src/multiqc.sh $input $input_fastp $output
 </code>