rename rule multiqc_raw_listing_files, set message for rule fastqc_raw and...

rename rule multiqc_raw_listing_files, set message for rule fastqc_raw and change directory to store ourput of rule multiqc_raw_list_files

rules/rawQC.smk

@@ -5,7 +5,7 @@ Description: rules for QC and pre-processing of paired-end shotgun DNA
 metagenomic sequencing.
 '''
 localrules:
-    multiqc_raw_listing_files,
+    multiqc_raw_list_files,
     multiqc_raw
 
 ##---------------------------------------------------------------------------##
@@ -33,22 +33,24 @@ rule fastqc_raw:
         fastqc_zip = RAW_QC_DIR+'/{dataset}_fastqc/{fastq_file}_fastqc.zip'
     threads: cpus_avail
     singularity: singularity_img
+    message:
+        "Executing FatQC on {input} with {threads} threads and using {params.samplerate} times total reads."
     shell:
         '''
-        # Take a random sample of reads (1%) and process them with fastQC
+        # Take a random sample of reads and process them with fastQC
         (reformat.sh in={input} out=stdout.fq samplerate={params.samplerate} | \
         fastqc -o {params.fastqc_dir}/{wildcards.dataset}_fastqc -f fastq \
         -t {threads} stdin:{wildcards.fastq_file}) 2> {log}
         '''
 
 # List files for MultiQC
-rule multiqc_raw_listing_files:
+rule multiqc_raw_list_files:
     input:
-        #all fastqc zip files in a dataset
+        #all fastqc zip files per dataset
         fastqcs=lambda wildcards: ['{}/{}_fastqc/{}_fastqc.zip'.format(RAW_QC_DIR, value, FASTQS[ix])
         for ix,value in enumerate(DATASETSX) if value==wildcards.dataset]
     output:
-        multiqc_input_list = RAW_QC_DIR+'/{dataset}_multiqc_inputs.txt'
+        multiqc_input_list = RAW_QC_REPORT+'/{dataset}_multiqc_inputs.txt'
     run:
         import os
         try:
@@ -59,10 +61,11 @@ rule multiqc_raw_listing_files:
         with open(output.multiqc_input_list, mode='w', encoding='utf-8') as out:
             for item in input.fastqcs:
                 out.write("%s\n" % item)
-#
+
+# Run MultiQC on all FastQC eports
 rule multiqc_raw:
     input:
-        RAW_QC_DIR+'/{dataset}_multiqc_inputs.txt'
+        RAW_QC_REPORT + '/{dataset}_multiqc_inputs.txt'
     output:
         multiqc_report = report(RAW_QC_REPORT + '/{dataset}_multiqc.html',
         category='rawQC')