added qualimap

tutorial/workflow/Snakefile

@@ -6,16 +6,12 @@ samples = pd.read_table(config["samples"], index_col="sample")
 
 rule all:
    input:
-        expand("results/trimmed/{sample}_forward_paired.fq.gz", sample=samples.index),
-        expand("results/trimmed/{sample}_forward_unpaired.fq.gz", sample=samples.index),
-        expand("results/trimmed/{sample}_reverse_paired.fq.gz", sample=samples.index),
-        expand("results/trimmed/{sample}_reverse_unpaired.fq.gz", sample=samples.index),
-        "results/aggregate/mappedcounts.csv",
         expand("results/stats/{sample}.stats.txt", sample=samples.index),
-        expand("results/fastqc/{sample}_1_fastqc.html", sample=samples.index),
-        expand("results/fastqc/{sample}_1_fastqc.zip", sample=samples.index),
-        expand("results/fastqc/{sample}_2_fastqc.html", sample=samples.index),
-        expand("results/fastqc/{sample}_2_fastqc.zip", sample=samples.index)
+        expand("results/fastqc/trimmed/{sample}_1_fastqc.html", sample=samples.index),
+        expand("results/fastqc/trimmed/{sample}_1_fastqc.zip", sample=samples.index),
+        expand("results/fastqc/trimmed/{sample}_2_fastqc.html", sample=samples.index),
+        expand("results/fastqc/trimmed/{sample}_2_fastqc.zip", sample=samples.index),
+        expand("results/qualimap/{sample}/qualimapReport.html", sample=samples.index)
 
 include:"rules/fastqc.smk"
 
@@ -26,3 +22,5 @@ include:"rules/samtools.smk"
 include:"rules/aggregate.smk"
 
 include:"rules/trimming.smk"
+
+include:"rules/qualimap.smk"

tutorial/workflow/envs/yourenv.yaml

@@ -23,6 +23,7 @@ dependencies:
   - perl=5.26.2=h4e221da_0
   - pip=21.2.2=py37hecd8cb5_0
   - python=3.7.11=h88f2d9e_0
+  - qualimap=2.2.2a
   - readline=8.1.2=hca72f7f_1
   - samtools=1.3.1=0
   - setuptools=58.0.4=py37hecd8cb5_0

tutorial/workflow/rules/qualimap.smk

+rule qualimap:
+    input:
+        "results/bam_sorted/{sample}.sorted.bam"
+    output:
+        "results/qualimap/{sample}/qualimapReport.html"
+    conda:
+        "../envs/yourenv.yaml"
+    log:
+        "workflow/report/qualimap/{sample}.log"
+    shell:
+        "qualimap bamqc -bam {input} -outdir results/qualimap/{wildcards.sample} 2> {log}"