fix#2

tutorial/workflow/envs/yourenv.yaml

@@ -9,6 +9,7 @@ dependencies:
   - ca-certificates=2022.2.1=hecd8cb5_0
   - certifi=2021.10.8=py37hecd8cb5_2
   - curl=7.80.0=hca72f7f_0
+  - fastqc=0.11.9
   - krb5=1.19.2=hcd88c3b_0
   - libcurl=7.80.0=h6dfd666_0
   - libcxx=12.0.0=h2f01273_0

tutorial/workflow/rules/fastqc.smk

+#map_dict = {'1':'fq1', '2':'fq2'}
+
+#rule rawfastqc:
+  #input:
+      #rf1 = lambda wildcards: samples.at[wildcards.sample,map_dict[wildcards.i]] if wildcards.sample in samples.index else ' '
+      #rf2 = lambda wildcards: samples.at[wildcards.sample,map_dict[wildcards.i]] if wildcards.sample in samples.index else ' '
+  #output:
+      #html="results/fastqc/{sample}_{i}_fastqc.html",
+      #zip="results/fastqc/{sample}_{i}_fastqc.zip"
+  #conda:
+      #"../envs/yourenv.yaml"
+  #log:
+      #"workflow/report/fastqc/{sample}_{i}.log"
+  #wrapper:
+      #"v1.3.1/bio/fastqc"
+
 rule rawfastqc1:
   input:
       rf1 = lambda wildcards: samples.at[wildcards.sample,'fq1'] if wildcards.sample in samples.index else ' '
   output:
-      html="results/fastqc/{sample}_1_fastqc.html",
-      zip="results/fastqc/{sample}_1_fastqc.zip"
+      html="results/fastqc/raw/{sample}_1_fastqc.html",
+      zip="results/fastqc/raw/{sample}_1_fastqc.zip"
   conda:
       "../envs/yourenv.yaml"
   log:
@@ -11,15 +27,46 @@ rule rawfastqc1:
   wrapper:
       "v1.3.1/bio/fastqc"
 
+
 rule rawfastqc2:
   input:
       rf2 = lambda wildcards: samples.at[wildcards.sample,'fq2'] if wildcards.sample in samples.index else ' '
   output:
-      html="results/fastqc/{sample}_2_fastqc.html",
-      zip="results/fastqc/{sample}_2_fastqc.zip"
+      html="results/fastqc/raw/{sample}_2_fastqc.html",
+      zip="results/fastqc/raw/{sample}_2_fastqc.zip"
   conda:
       "../envs/yourenv.yaml"
   log:
       "workflow/report/fastqc/{sample}.log"
   wrapper:
       "v1.3.1/bio/fastqc"
+
+
+rule trimmedfastqc1:
+    input:
+        "results/trimmed/{sample}_forward_paired.fq.gz",
+        "results/trimmed/{sample}_reverse_paired.fq.gz"
+    output:
+        html="results/fastqc/trimmed/{sample}_1_fastqc.html",
+        zip="results/fastqc/trimmed/{sample}_1_fastqc.zip"
+    conda:
+        "../envs/yourenv.yaml"
+    log:
+        "workflow/report/fastqc/trimmed_{sample}.log"
+    wrapper:
+        "v1.3.1/bio/fastqc"
+
+
+rule trimmedfastqc2:
+    input:
+        "results/trimmed/{sample}_forward_paired.fq.gz",
+        "results/trimmed/{sample}_reverse_paired.fq.gz"
+    output:
+        html="results/fastqc/trimmed/{sample}_2_fastqc.html",
+        zip="results/fastqc/trimmed/{sample}_2_fastqc.zip"
+    conda:
+        "../envs/yourenv.yaml"
+    log:
+        "workflow/report/fastqc/trimmed_{sample}.log"
+    wrapper:
+        "v1.3.1/bio/fastqc"