Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into ac…

…tiveDev updating
CCBR · Aug 24, 2018 · 1da27b4 · 1da27b4
2 parents 98b2e8b + dc3340f
commit 1da27b4
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Showing 4 changed files with 5 additions and 1 deletion.
diff --git a/PipelinerVer1.0_documentation.docx b/PipelinerVer1.0_documentation.docx
diff --git a/PipelinerVer1.0_documentation.pdf b/PipelinerVer1.0_documentation.pdf
diff --git a/Rules/InitialChIPseqQC.snakefile b/Rules/InitialChIPseqQC.snakefile
@@ -748,17 +748,20 @@ rule multiqc:
         expand(join(workpath,bam_dir,"{name}.bwa.Q5.duplic"), name=samples),
         expand(join(workpath,"FQscreen","{name}.R1.trim_screen.txt"),name=samples),
         expand(join(workpath,preseq_dir,"{name}.ccurve"), name=samples),
+	expand(join(workpath,bam_dir,"{name}.sorted.Q5DD.bam.flagstat"), name=samples),
+	expand(join(workpath,bam_dir,"{name}.sorted.Q5.bam.flagstat"), name=samples),
         join(workpath,"QC"),
         join(workpath,"rawQC"),            
     output:
         join(workpath,"Reports","multiqc_report.html")
     params:
         rname="pl:multiqc",
         multiqc=config['bin'][pfamily]['tool_versions']['MULTIQCVER'],
+	qcconfig=config['bin'][pfamily]['CONFMULTIQC'],
     threads: 1
     shell: """
 module load {params.multiqc}
-cd Reports && multiqc -f --interactive -e cutadapt -d ../
+cd Reports && multiqc -f -c {params.qcconfig} --interactive -e cutadapt -d ../
 """
 
 
diff --git a/standard-bin.json b/standard-bin.json
@@ -349,6 +349,7 @@
         "BOWTIE2VER": "bowtie/2-2.3.4",
         "BWAVER": "bwa/0.7.17",
         "CUTADAPTVER": "cutadapt/1.16",
+        "CONFMULTIQC": "/data/CCBR_Pipeliner/db/PipeDB/ChIPseq/multiqc_config.yaml",
         "DEEPTOOLSVER": "deeptools/3.0.1",
         "FASTQ_SCREEN": "/data/CCBR_Pipeliner/db/PipeDB/bin/fastq_screen_v0.9.3/fastq_screen",
         "FASTQCVER": "fastqc/0.11.5",