updated config files

dunnart/configs/.multiqc_config.yaml

@@ -2,6 +2,15 @@ title: "Histone ChIP-seq QC for dunnart craniofacial tissue: H3K4me3 & H3K27ac"
 intro_text: ""
 report_comment: "Generated on DATE"
 
+run_modules:
+    - custom_content
+    - fastqc
+    - samtools
+    - picard
+    - preseq
+    - deeptools
+    - phantompeakqualtools
+
 
 report_header_info:
     - Contact E-mail: 'lecook@student.unimelb.edu.au'
@@ -10,12 +19,12 @@ report_header_info:
 module_order:
     - MACS2
     - MACS2_narrowPeak_count
-    - deepTools
-    - Preseq:
+    - deeptools
+    - preseq:
         genome_size: 3074798085
         read_length: 150
-    - Samtools
-    - Picard
+    - samtools
+    - picard
     - phantompeakqualtools
     - bowtie2:
         name: 'Bowtie2'
@@ -24,33 +33,84 @@ module_order:
 
 log_filesize_limit: 5000000000
 
-custom_data:
-    encode_metrics:
-        plot_type: 'generalstats'
-        file_format: 'tsv'
-        pconfig:
-            - NRF:
-                namespace: "NRF"
-                title: "NRF"
-                description: "ratio between the number of positions in the genome that uniquely mapped reads map to and the total number of uniquely mappable reads"
-                max: 1
-                min: 0
-                scale: 'RdYlGn'
-            - PBC1:
-                namespace: "PBC1"
-                title: "PBC1"
-                description: "ratio of genomic locations with EXACTLY one read pair over the genomic locations with AT LEAST one read pair"
-                max: 1
-                min: 0
-                scale: 'RdYlGn'
-            - PBC2:
-                namespace: "PBC2"
-                title: "PBC2"
-                description: "ratio of genomic locations with EXACTLY one read pair over the genomic locations with EXACTLY two read pairs"
-                max: 10
-                min: 0
-                scale: 'RdYlGn'
+id: 'frip_score'
+section_name: 'MACS2 FRiP score'
+plot_type: 'bargraph'
+anchor: 'frip_score'
+pconfig:
+   title: 'FRiP score'
+   ylab: 'FRiP score'
+   ymax: 1
+   ymin: 0
+   tt_decimals: 2
+
+id: 'peak_count'
+section_name: 'MACS2 peak count'
+description: "is calculated from total number of peaks called by
+	       <a href='https://github.com/taoliu/MACS' target='_blank'>MACS2</a>"
+plot_type: 'bargraph'
+anchor: 'peak_count'
+pconfig:
+   title: 'Total peak count'
+   ylab: 'Peak count'
+
+id: 'strand_shift_correlation'
+section_name: 'spp strand-shift correlation'
+description: "generated using run_spp.R script from
+             <a href='https://github.com/kundajelab/phantompeakqualtools' target='_blank'>phantompeakqualtools</a>."
+plot_type: 'linegraph'
+anchor: 'strand_shift_correlation'
+pconfig:
+   title: 'Strand-shift correlation plot'
+   ylab: 'Cross-correlation'
+   xlab: 'Strand-shift (bp)'
+   xDecimals: False
+   tt_label: 'Strand-shift (bp) {point.x}: {point.y:.2f} Cross-correlation'
+
+id: 'nsc_coefficient'
+section_name: 'spp NSC coefficient'
+description: "generated using run_spp.R script from
+             <a href='https://github.com/kundajelab/phantompeakqualtools' target='_blank'>phantompeakqualtools</a>."
+plot_type: 'bargraph'
+anchor: 'nsc_coefficient'
+pconfig:
+   title: 'Normalized strand cross-correlation coefficient'
+   ylab: 'NSC coefficient'
+   ymin: 1
+   tt_decimals: 1
+
+id: 'rsc_coefficient'
+section_name: 'spp RSC coefficient'
+description: "generated using run_spp.R script from
+             <a href='https://github.com/kundajelab/phantompeakqualtools' target='_blank'>phantompeakqualtools</a>."
+plot_type: 'bargraph'
+anchor: 'rsc_coefficient'
+pconfig:
+   title: 'Relative strand cross-correlation coefficient'
+   ylab: 'RSC coefficient'
+   ymin: 0
+   tt_decimals: 1
+
+
+report_section_order:
+    frip_score:
+        before: peak_count
+    strand_shift_correlation:
+        before: peak_annotation
+    nsc_coefficient:
+        before: strand_shift_correlation
+    rsc_coefficient:
+        before: nsc_coefficient
+
+custom_plot_config:
+    picard_insert_size:
+        cpswitch_c_active: False
+        smooth_points: 1000
 
 sp:
-    encode_metrics:
-        fn: '*encodeQC.txt'
+    preseq:
+        fn: '*.ccurve.txt'
+    deeptools/plotFingerprintOutRawCounts:
+        fn: '*plotFingerprint*'
+    deeptools/plotProfile:
+        fn: '*plotProfile*'

dunnart/configs/SRR.txt

-IP	Input
-A-2_H3K4me3	A-1_input
-A-3_H3K27ac	A-1_input
-B-2_H3K4me3	B-1_input
-B-3_H3K27ac	B-1_input
+IP      Input   mark
+A-2_H3K4me3     A-1_input       H3K4me3
+A-3_H3K27ac     A-1_input       H3K27ac
+B-2_H3K4me3     B-1_input       H3K4me3
+B-3_H3K27ac     B-1_input       H3K27ac