From e0c32f0d3ebd140dcf2859869bdadcdf55e35243 Mon Sep 17 00:00:00 2001
From: Catherine Chahrour <74187550+CChahrour@users.noreply.github.com>
Date: Tue, 27 Feb 2024 11:04:18 +0000
Subject: [PATCH] Remove wrappers from rules (#144)

* remove wrapper from fastqc

* fix multiqc rule
---
 seqnado/workflow/rules/qc.smk | 61 ++++++++++++++++++++++++-----------
 1 file changed, 43 insertions(+), 18 deletions(-)

diff --git a/seqnado/workflow/rules/qc.smk b/seqnado/workflow/rules/qc.smk
index b2164846..6c7f95d1 100644
--- 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",
 
@@ -108,7 +133,7 @@ def get_fastqc_files(*args, **kwargs):
     fastqc_files = []
     fq_files = pathlib.Path("seqnado_output/fastqs").glob("*.fastq.gz")
     for fq_file in fq_files:
-        fastqc_file = fastqc_dir / (fq_file.stem.replace(".fastq", "") + ".html")
+        fastqc_file = fastqc_dir / (fq_file.stem.replace(".fastq", "") + "_fastqc.html")
         fastqc_files.append(str(fastqc_file))
 
     return fastqc_files
@@ -136,7 +161,7 @@ def get_trimmed_files(wc):
     fastqc_files = []
     fq_files = pathlib.Path("seqnado_output/fastqs").glob("*.fastq.gz")
     for fq_file in fq_files:
-        fastqc_file = fastqc_dir / (fq_file.stem.replace(".fastq", "") + ".html")
+        fastqc_file = fastqc_dir / (fq_file.stem.replace(".fastq", "") + "_fastqc.html")
         fastqc_files.append(str(fastqc_file))
 
     return fastqc_files