Update fastqc rule

Author: xies4

rules/fastqc4QC.smk

@@ -1,17 +1,23 @@
-
+import os
+print(record_fastqpath)
 rule fastqc4QC:
+    # input: 
+    #     log_prep_fq = rules.prep_fastq_folder.output.log
     params: 
-        prefix = "{sample}", 
-        prefix2 = filterFastq4nopipe, 
-        fastqc_outdir = "QC/Sample_{sample}/fastqc_outdir"
+        fastqc_outdir = os.path.join(analysis, "QC/Sample_{sample}/fastqc_outdir"),
+        fastq_path = lambda wildcards: record_fastqpath[wildcards.sample],
     output: 
-        "QC/Sample_{sample}/fastqc_outdir/fastqc.log"
+        os.path.join(analysis, "QC/Sample_{sample}/fastqc_outdir/fastqc.log")
     container:
         program.fastqc
     threads: 8 # could be overwritten by the config file
     shell:
         """
-        # find all the fastq files in the sample directory and perform fastqc on them
-        fastq_files=$(find {params.prefix} -name "*.fastq.gz")
-        fastqc --threads {threads} --outdir={params.fastqc_outdir} $fastq_files >{output} 2>&1
-        """
+        mkdir -p {params.fastqc_outdir}
+        echo "Running FastQC in the folder of: "
+        pwd
+        fastq_files=$(find {params.fastq_path} -name "*.fastq.gz" -or -name "*.fq.gz")
+        fastqc --threads {threads} \
+               --outdir={params.fastqc_outdir} \
+               $fastq_files >{output} 2>&1
+        """