adding more variables

Author: Joon-Klaps

assets/custom_table_headers.yml

@@ -7,9 +7,9 @@ failed_mapped:
   - error_rate: "error rate"
   - mismatches: "mismatches"
   - reads_MQ0: "reads MQ0"
-  - reads_mapped: "reads mapped"
+  - reads_mapped: "reads mapped (R1+R2)"
   - reads_mapped_percent: "reads mapped %"
-  - reads_unmapped: "reads unmapped"
+  - reads_unmapped: "reads unmapped (R1+R2)"
   - reads_unmapped_percent: "reads unmapped %"
   - reads_QC_failed: "reads QC failed"
   - reads_QC_failed_percent: "reads QC failed %"
@@ -31,9 +31,9 @@ failed_mapped:
   - bases_duplicated: "bases duplicated"
 umitools:
   - multiqc_umitools_dedup:
-      - dedup_input_reads: "mapped reads"
-      - dedup_removed_reads: "removed reads"
-      - dedup_output_reads: "deduplicated reads"
+      - dedup_input_reads: "mapped reads (R1,R2)"
+      - dedup_removed_reads: "removed reads (R1,R2)"
+      - dedup_output_reads: "deduplicated reads (R1,R2)"
       - positions_deduplicated: "positions deduplicated"
       - max_umi_per_pos: "max UMI per position"
       - mean_umi_per_pos: "mean UMI per position"
@@ -44,7 +44,7 @@ picard:
   - multiqc_picard_dups:
       - UNPAIRED_READS_EXAMINED: "unpaired reads examined"
       - READ_PAIR_OPTICAL_DUPLICATES: "read pair optical duplicates"
-      - UNMAPPED_READS: "unmapped reads"
+      - UNMAPPED_READS: "unmapped reads (R1+R2)"
       - ESTIMATED_LIBRARY_SIZE: "estimated library size"
       - UNPAIRED_READ_DUPLICATES: "unpaired read duplicates"
       - SECONDARY_OR_SUPPLEMENTARY_RDS: "secondary or supplementary rds"
@@ -60,9 +60,9 @@ picard:
       - error_rate: "error rate"
       - mismatches: "mismatches"
       - reads_MQ0: "reads MQ0"
-      - reads_mapped: "reads mapped"
+      - reads_mapped: "reads mapped (R1+R2)"
       - reads_mapped_percent: "reads mapped %"
-      - reads_unmapped: "reads unmapped"
+      - reads_unmapped: "reads unmapped (R1+R2)"
       - reads_unmapped_percent: "reads unmapped %"
       - reads_QC_failed: "reads QC failed"
       - reads_QC_failed_percent: "reads QC failed %"

bin/utils/constant_variables.py

@@ -29,6 +29,17 @@
         'namespace_patterns': 'fastp',
         'suffix': 'R1+R2'
     },
+    'unique reads': {
+        'namespace_patterns': 'humid',
+        'suffix': 'R1,R2'
+    },
+    'reads assigned': {
+        'namespace_patterns': 'kaiju',
+        'suffix': 'R1+R2'
+    }
+    #TODO:
+    # - prinseq ++
+    # - bbduk
 
 }