[Documentation] Update qc_check documentation (#1014)

Author: nehavm456

docs/common_text/qc_check_task.md

@@ -8,7 +8,7 @@
 <!-- if: theiacov -->
     The `qc_check` task applies quality thresholds according to the specified organism, which should match the _standardized_ `organism` input in the TheiaCoV workflows.
 
-    Segment-based QC can be applied to influenza genomes for "percent_reference_coverage", "median_coverage", and "num_minor_snv". To apply thresholds across all individual segments, use "segment_" as a prefix for the QC threshold column in the QC check template. To apply thresholds to individual segments, use the following prefixes: "mp_", "pb1_", "pb2_", "na_", "ns_", "np_", "pa_", and "ha_". Segment-specific thresholds are preferentially used over general segment thresholds if both are present. 
+    Segment-based QC can be applied to influenza genomes for "percent_reference_coverage", "median_coverage", and "num_minor_snv". To apply thresholds across all segments, use "segment_" as a prefix for the QC threshold column in the QC check template. To apply thresholds to individual segments, use the following prefixes: "mp_", "pb1_", "pb2_", "na_", "ns_", "np_", "pa_", and "ha_". For example, percent reference coverage for the mp segment should have a column labeled `mp_percent_reference_coverage`. Segment-specific thresholds are preferentially used over general segment thresholds if both are present. If all segment-specific thresholds are provided for a metric, the general segment threshold for that metric should be left blank. Otherwise, the `qc_check` output will contain a `QC_ALERT` message. If some segment-specific thresholds are provided for a metric, the general segment threshold will only be used for segments that do not have a provided threshold.
 <!-- endif -->
 <!-- if: theiaprok|theiaeuk -->
     The `qc_check` task applies quality thresholds according to the sample taxa. The sample taxa is taken from the `gambit_predicted_taxon` value inferred by the GAMBIT module OR can be manually provided by the user using the `expected_taxon` workflow input.