remove wrapper from fastqc

alsmith151 · Feb 14, 2024 · a5d850f · a5d850f
1 parent 116eec6
commit a5d850f
Showing 1 changed file with 41 additions and 16 deletions.
diff --git a/seqnado/workflow/rules/qc.smk b/seqnado/workflow/rules/qc.smk
@@ -4,49 +4,74 @@ import seqnado.utils
 
 rule fastqc_raw_paired:
     input:
-        "seqnado_output/fastqs/{sample}_{read}.fastq.gz",
+        fq1="seqnado_output/fastqs/{sample}_1.fastq.gz",
+        fq2="seqnado_output/fastqs/{sample}_2.fastq.gz",
     output:
-        html="seqnado_output/qc/fastqc_raw/{sample}_{read}.html",
-        zip="seqnado_output/qc/fastqc_raw/{sample}_{read}_fastqc.zip",  # the suffix _fastqc.zip is necessary for multiqc to find the file. If not using multiqc, you are free to choose an arbitrary filename
+        html1="seqnado_output/qc/fastqc_raw/{sample}_1_fastqc.html",
+        html2="seqnado_output/qc/fastqc_raw/{sample}_2_fastqc.html",
+        zip1="seqnado_output/qc/fastqc_raw/{sample}_1_fastqc.zip",
+        zip2="seqnado_output/qc/fastqc_raw/{sample}_2_fastqc.zip",
     params:
         extra="--quiet",
+        output_dir="seqnado_output/qc/fastqc_raw/",
+        temp_prefix="seqnado_output/qc/fastqc_raw/{sample}",
     threads: 1
     resources:
         mem_mb=1500,
     log:
-        "seqnado_output/logs/fastqc_raw/{sample}_{read}.log",
-    wrapper:
-        "v3.0.1/bio/fastqc"
+        "seqnado_output/logs/fastqc_raw/{sample}.log",
+    shell:
+        """
+        fastqc -o {params.output_dir} {input.fq1} {input.fq2}
+        """
+
 
 
 rule fastqc_raw_single:
     input:
         "seqnado_output/fastqs/{sample}.fastq.gz",
     output:
-        html="seqnado_output/qc/fastqc_raw/{sample}.html",
-        zip="seqnado_output/qc/fastqc_raw/{sample}_fastqc.zip",  # the suffix _fastqc.zip is necessary for multiqc to find the file. If not using multiqc, you are free to choose an arbitrary filename
+        html="seqnado_output/qc/fastqc_raw/{sample}_fastqc.html",
+        zip="seqnado_output/qc/fastqc_raw/{sample}_fastqc.zip",
+    params:
+        extra="--quiet",
+        output_dir='seqnado_output/qc/fastqc_raw/',
+        temp_prefix="seqnado_output/qc/fastqc_raw/{sample}",
     log:
         "seqnado_output/logs/fastqc_raw/{sample}.log",
-    wrapper:
-        "v3.0.1/bio/fastqc"
+    shell:
+        """
+        fastqc -o {params.output_dir} {input}
+        """
 
 
 use rule fastqc_raw_paired as fastqc_trimmed_paired with:
     input:
-        "seqnado_output/trimmed/{sample}_{read}.fastq.gz",
+        fq1="seqnado_output/trimmed/{sample}_1.fastq.gz",
+        fq2="seqnado_output/trimmed/{sample}_2.fastq.gz",
     output:
-        html="seqnado_output/qc/fastqc_trimmed/{sample}_{read}.html",
-        zip="seqnado_output/qc/fastqc_trimmed/{sample}_{read}_fastqc.zip",  # the suffix _fastqc.zip is necessary for multiqc to find the file. If not using multiqc, you are free to choose an arbitrary filename
+        html1="seqnado_output/qc/fastqc_trimmed/{sample}_1_fastqc.html",
+        html2="seqnado_output/qc/fastqc_trimmed/{sample}_2_fastqc.html",
+        zip1="seqnado_output/qc/fastqc_trimmed/{sample}_1_fastqc.zip",
+        zip2="seqnado_output/qc/fastqc_trimmed/{sample}_2_fastqc.zip",
+    params:
+        extra="--quiet",
+        output_dir='seqnado_output/qc/fastqc_trimmed/',
+        temp_prefix="seqnado_output/qc/fastqc_trimmed/{sample}",
     log:
-        "seqnado_output/logs/fastqc_trimmed/{sample}_{read}.log",
+        "seqnado_output/logs/fastqc_trimmed/{sample}.log",
 
 
 use rule fastqc_raw_single as fastqc_trimmed_single with:
     input:
         "seqnado_output/trimmed/{sample}.fastq.gz",
     output:
-        html="seqnado_output/qc/fastqc_trimmed/{sample}.html",
-        zip="seqnado_output/qc/fastqc_trimmed/{sample}_fastqc.zip",  # the suffix _fastqc.zip is necessary for multiqc to find the file. If not using multiqc, you are free to choose an arbitrary filename
+        html="seqnado_output/qc/fastqc_trimmed/{sample}_fastqc.html",
+        zip="seqnado_output/qc/fastqc_trimmed/{sample}_fastqc.zip", 
+    params:
+        extra="--quiet",
+        output_dir='seqnado_output/qc/fastqc_trimmed/',
+        temp_prefix="seqnado_output/qc/fastqc_trimmed/{sample}",
     log:
         "seqnado_output/logs/fastqc_trimmed/{sample}.log",