switches qc-checkup to quac_watch - contd

Changelog.md

@@ -22,10 +22,10 @@ YYYY-MM-DD  John Doe
 
 * QuaC is heavily reworked to be a companion pipeline to small variant caller pipeline and will now perform most of the
   QC analyses for WGS/WES data. While the small caller pipeline will still run few QC tools (for pragmatic reasons),
-  QuaC will now take over the heavylifting of QC, including the QC-checkup.
+  QuaC will now take over the heavylifting of QC, including the QC-checkup, which is now called as QuaC-Watch.
 * QuaC can perform both sample-level and project-level QC. This is the major reason why it was decided to separate QC from small-variant caller pipeline, as it could only perform single-sample QC.
 * More QC tools were added
-* For QC checkup, QuaC now heavily expands to vcf metrics and adds significant amount of QC thresholds for bam metrics.
+* For QC checkup (ie. QuaC-Watch), QuaC now heavily expands to vcf metrics and adds significant amount of QC thresholds for bam metrics.
 * QuaC's input are output from the small variant caller pipeline, and former's output will fit seemlessly with the latter's output.
 * QuaC accepts pedigree file as input. A dummy pedigree file creator script is provided, which will be handy until phenotips is made available to us.
 * System-level testing is added

configs/multiqc_config.yaml

@@ -31,7 +31,7 @@ table_columns_placement:
 
 # order of modules to show in report
 module_order:
-    - cgds_qc_checkup
+    - cgds_quac_watch
     - qualimap
     - picard
     - samtools
@@ -71,40 +71,40 @@ qualimap_config:
         - 200
 
 # configs for CGDS QC check-ups
-# NOTE: This multiqc config file has hard-coded parameters, which is based on the QC-checkup config file.
-# If parameters in QC-checkup config file get modified, this file may need to be edited correspondingly.
+# NOTE: This multiqc config file has hard-coded parameters, which is based on the QuaC-Watch config file.
+# If parameters in QuaC-Watch config file get modified, this file may need to be edited correspondingly.
 custom_data:
-    qc_checkup_overall_summary:
-        parent_id: "cgds_qc_checkup"
-        parent_name: "CGDS - QC checkup"
+    quac_watch_overall_summary:
+        parent_id: "cgds_quac_watch"
+        parent_name: "CGDS - QuaC-Watch"
         parent_description: "This section contains CGDS's QC checking results (Might not work well for WES)."
-        id: "qc_checkup_overall_summary"
-        section_name: "Overall QC checkup summary"
-        description: "Overall QC checkup summary of results from several QC tools"
+        id: "quac_watch_overall_summary"
+        section_name: "Overall QuaC-Watch summary"
+        description: "Overall QuaC-Watch summary of results from several QC tools"
         file_format: "yaml"
         plot_type: "table"
         pconfig:
-            table_title: "Overall QC checkup summary"
+            table_title: "Overall QuaC-Watch summary"
 
-    qc_checkup_fastqc:
-        parent_id: "cgds_qc_checkup"
-        id: "qc_checkup_fastqc"
+    quac_watch_fastqc:
+        parent_id: "cgds_quac_watch"
+        id: "quac_watch_fastqc"
         section_name: "FastQC (trimmed)"
         description: 'Quick summary of FastQC (trimmed) results. See <a href="#trimmed">FastQC</a> section below for detailed results.'
         file_format: "yaml"
         plot_type: "table"
         pconfig:
-            table_title: "FastQC - QC checkup"
+            table_title: "FastQC - QuaC-Watch"
 
-    qc_checkup_qualimap_overall:
-        parent_id: "cgds_qc_checkup"
-        id: "qc_checkup_qualimap_overall"
+    quac_watch_qualimap_overall:
+        parent_id: "cgds_quac_watch"
+        id: "quac_watch_qualimap_overall"
         section_name: "Qualimap - Overall stats"
         description: 'Quick summary of Qualimap results. See <a href="#qualimap">QualiMap</a> section below for detailed results.'
         file_format: "yaml"
         plot_type: "table"
         pconfig:
-            table_title: "Qualimap - Overall stats - QC checkup"
+            table_title: "Qualimap - Overall stats - QuaC-Watch"
             only_defined_headers: False
             scale: "Blues"
         headers:
@@ -113,7 +113,7 @@ custom_data:
                 max: 42.5
                 description: "Mean GC content (min: 40.5, max: 42.5)"
                 hidden: True
-            # if you change coverage limits, also change values in "qc_checkup_qualimap_chromosome_stats"
+            # if you change coverage limits, also change values in "quac_watch_qualimap_chromosome_stats"
             mean_coverage_val:
                 min: 100
                 description: "Mean coverage (min: 100)"
@@ -142,15 +142,15 @@ custom_data:
                 description: "Alignment error rate (min: 0, max: 0.8)"
                 hidden: True
 
-    qc_checkup_qualimap_chromosome_stats:
-        parent_id: "cgds_qc_checkup"
-        id: "qc_checkup_qualimap_chromosome_stats"
+    quac_watch_qualimap_chromosome_stats:
+        parent_id: "cgds_quac_watch"
+        id: "quac_watch_qualimap_chromosome_stats"
         section_name: "Qualimap - Chromosome stats"
         description: 'Quick summary chromosome-level coverage info using Qualimap results. See <a href="#qualimap">QualiMap</a> section below for detailed results.'
         file_format: "yaml"
         plot_type: "linegraph"
         pconfig:
-            id: qc_checkup_qualimap_chromosome_stats
+            id: quac_watch_qualimap_chromosome_stats
             ymin: 0
             ymax: 100
             categories: True
@@ -162,15 +162,15 @@ custom_data:
                 showInLegend: False
                 color: "PaleVioletRed"
 
-    qc_checkup_picard:
-        parent_id: "cgds_qc_checkup"
-        id: "qc_checkup_picard"
+    quac_watch_picard:
+        parent_id: "cgds_quac_watch"
+        id: "quac_watch_picard"
         section_name: "Picard"
         description: 'Quick summary of picard metrics. Note: Picard-Duplication is reported separately (bcoz reasons!).  See <a href="#picard-1">Picard</a> section below for detailed results.'
         file_format: "yaml"
         plot_type: "table"
         pconfig:
-            table_title: "Picard - Overall stats - QC checkup"
+            table_title: "Picard - Overall stats - QuaC-Watch"
             only_defined_headers: False
             scale: "Blues"
         headers:
@@ -228,15 +228,15 @@ custom_data:
             PCT_15X:
                 description: "% of bases that attained at least 15X sequence coverage in post-filtering bases."
 
-    qc_checkup_picard_dups:
-        parent_id: "cgds_qc_checkup"
-        id: "qc_checkup_picard_dups"
+    quac_watch_picard_dups:
+        parent_id: "cgds_quac_watch"
+        id: "quac_watch_picard_dups"
         section_name: "Picard-dups"
         description: 'Quick summary of picard-duplication metrics. See <a href="#picard-1">Picard</a> section below for detailed results.'
         file_format: "yaml"
         plot_type: "table"
         pconfig:
-            table_title: "Picard duplication - Overall stats - QC checkup"
+            table_title: "Picard duplication - Overall stats - QuaC-Watch"
             only_defined_headers: False
             scale: "Blues"
         headers:
@@ -246,15 +246,15 @@ custom_data:
                 description: "% of mapped reads that are marked as duplicates (min: 0, max: 15)"
                 hidden: True
 
-    qc_checkup_bcftools_stats:
-        parent_id: "cgds_qc_checkup"
-        id: "qc_checkup_bcftools_stats"
+    quac_watch_bcftools_stats:
+        parent_id: "cgds_quac_watch"
+        id: "quac_watch_bcftools_stats"
         section_name: "Bcftools stats"
         description: 'Quick summary of Bcftools-stats results. See <a href="#bcftools">Bcftools</a> section below for detailed results.'
         file_format: "yaml"
         plot_type: "table"
         pconfig:
-            table_title: "Bcftools stats - QC checkup"
+            table_title: "Bcftools stats - QuaC-Watch"
             only_defined_headers: False
             scale: "Blues"
         headers:
@@ -308,15 +308,15 @@ custom_data:
             heterozygosity_ratio:
                 description: "No. of het sites in an individual divided by the no. of non-reference hom sites. Note: This varies heavily across populations."
 
-    qc_checkup_variant_per_contig:
-        parent_id: "cgds_qc_checkup"
-        id: "qc_checkup_variant_per_contig"
+    quac_watch_variant_per_contig:
+        parent_id: "cgds_quac_watch"
+        id: "quac_watch_variant_per_contig"
         section_name: "Variant frequency per contig"
         description: "Quick summary of %variant per contig results."
         file_format: "yaml"
         plot_type: "table"
         pconfig:
-            table_title: "%Variant per contig - QC checkup"
+            table_title: "%Variant per contig - QuaC-Watch"
             only_defined_headers: False
             scale: "Blues"
         headers:
@@ -465,15 +465,15 @@ custom_data:
                 format: '{:,.6f}'
                 hidden: True
 
-    qc_checkup_verifybamid:
-        parent_id: "cgds_qc_checkup"
-        id: "qc_checkup_verifybamid"
+    quac_watch_verifybamid:
+        parent_id: "cgds_quac_watch"
+        id: "quac_watch_verifybamid"
         section_name: "VerifyBAMID"
         description: 'Quick summary of VerifyBAMID results. See <a href="#verifybamid-1">VerifyBAMID</a> section below for detailed results.'
         file_format: "yaml"
         plot_type: "table"
         pconfig:
-            table_title: "VerifyBAMID - QC checkup"
+            table_title: "VerifyBAMID - QuaC-Watch"
             only_defined_headers: False
             scale: "Blues"
         headers:
@@ -487,15 +487,15 @@ custom_data:
                 title: "Contamination(%)"
                 description: "% Cross-human-sample contamination"
 
-    qc_checkup_fastq_screen:
-        parent_id: "cgds_qc_checkup"
-        id: "qc_checkup_fastq_screen"
+    quac_watch_fastq_screen:
+        parent_id: "cgds_quac_watch"
+        id: "quac_watch_fastq_screen"
         section_name: "FastQ Screen (trimmed)"
         description: 'Quick summary of FastQ Screen (trimmed) results. See <a href="#fastq_screen-1">FastQ Screen</a> section below for detailed results.'
         file_format: "yaml"
         plot_type: "table"
         pconfig:
-            table_title: "FastQ Screen - QC checkup"
+            table_title: "FastQ Screen - QuaC-Watch"
             only_defined_headers: False
             scale: "Blues"
         headers:
@@ -590,23 +590,23 @@ custom_data:
 
 # define file pattern for custom configs
 sp:
-    qc_checkup_overall_summary:
-        fn: "qc_checkup_overall_summary.yaml"
-    qc_checkup_fastqc:
-        fn: "qc_checkup_fastqc.yaml"
-    qc_checkup_qualimap_overall:
-        fn: "qc_checkup_qualimap_overall.yaml"
-    qc_checkup_qualimap_chromosome_stats:
-        fn: "qc_checkup_qualimap_chromosome_stats.yaml"
-    qc_checkup_picard:
-        fn: "qc_checkup_picard.yaml"
-    qc_checkup_picard_dups:
-        fn: "qc_checkup_picard_dups.yaml"
-    qc_checkup_bcftools_stats:
-        fn: "qc_checkup_bcftools_stats.yaml"
-    qc_checkup_variant_per_contig:
-        fn: "qc_checkup_variant_per_contig.yaml"
-    qc_checkup_verifybamid:
-        fn: "qc_checkup_verifybamid.yaml"
-    qc_checkup_fastq_screen:
-        fn: "qc_checkup_fastq_screen.yaml"
\ No newline at end of file
+    quac_watch_overall_summary:
+        fn: "quac_watch_overall_summary.yaml"
+    quac_watch_fastqc:
+        fn: "quac_watch_fastqc.yaml"
+    quac_watch_qualimap_overall:
+        fn: "quac_watch_qualimap_overall.yaml"
+    quac_watch_qualimap_chromosome_stats:
+        fn: "quac_watch_qualimap_chromosome_stats.yaml"
+    quac_watch_picard:
+        fn: "quac_watch_picard.yaml"
+    quac_watch_picard_dups:
+        fn: "quac_watch_picard_dups.yaml"
+    quac_watch_bcftools_stats:
+        fn: "quac_watch_bcftools_stats.yaml"
+    quac_watch_variant_per_contig:
+        fn: "quac_watch_variant_per_contig.yaml"
+    quac_watch_verifybamid:
+        fn: "quac_watch_verifybamid.yaml"
+    quac_watch_fastq_screen:
+        fn: "quac_watch_fastq_screen.yaml"
\ No newline at end of file