From a8b0bec30f17d387fd49603fd6d2a597f6b00063 Mon Sep 17 00:00:00 2001
From: ticlla <monicaroxana.ticllaccenhua@unibas.ch>
Date: Mon, 10 Jun 2019 16:17:34 +0200
Subject: [PATCH] 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 | 17 ++++++++++-------
1 file changed, 10 insertions(+), 7 deletions(-)
diff --git a/rules/rawQC.smk b/rules/rawQC.smk
index 0f1997c..b835d0f 100644
--- a/rules/rawQC.smk
+++ b/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')
--
GitLab