add --expected_sequences_mismatches

Author: d4straub

conf/modules.config

@@ -1242,7 +1242,7 @@ process {
     }
 
     withName: COMPARE_PERFORMANCE {
-        ext.mismatch_threshold = 0 // thereshold for comparing matches (0=exact match)
+        ext.mismatch_threshold = { "${params.expected_sequences_mismatches}" } // thereshold for comparing matches (0=exact match)
         ext.fbeta = 2 // Fbeta weight, default 2; 1=precision and recall equally weighted (=F1 score), 2=weighs recall higher than precision, 0.5=weighs recall lower than precision.
         publishDir = [
             [

docs/output.md

@@ -658,9 +658,9 @@ On request (`--ancombc2`), ANCOM-BC2 is applied to each suitable or specified me
 
 </details>
 
-### Compare to expected
+### Compare observed to expected outcome
 
-Comparison evaluates observed results against expected outcomes, typically for samples with known composition such as mock communities, to assess the data and analysis. Steps to evaluate the produced ASVs are implemented in the pipeline.
+The observed results can be compared to expected outcomes per sample, typically for samples with known composition such as mock communities, to assess the performance of the data generation and analysis. Steps to evaluate the produced ASVs are implemented in the pipeline.
 
 When expected sequences are supplied, the following files will be produced:
 

docs/usage.md

@@ -344,8 +344,9 @@ The observed sequences will be aligned globally (using `VSEASRCH --usearch_globa
 Depending on the region to analyse (`--expected_sequences_region`) the mismatches and gaps within the alignment will be summarized with or without terminal gaps.
 The nucleotide differences will be evaluated for each observed sequence to its best match.
 
+Observed sequences will be accepted as "match" to an expected sequence (i.e. true positive) if there are no mismatches or gaps in the region (adjustable with `--expected_sequences_mismatches`).
 Expected abundances per sequence (`--expected_abundances`) enable sample specific presence/absence metrics and abundance-based comparisons.
-For those, observed and expected sequences will be aggregated by their analysed region: when one observed sequence matches exactely to several expected sequences, the expected sequence IDs will be concatenated and vice versa.
+For those, observed and expected sequences will be aggregated by their analysed region: when one observed sequence matches to several expected sequences, the expected sequence IDs will be concatenated and vice versa.
 That means, for example, if observed sequences are shorter than expected sequences and the analysed region is "query", each expected sequence (ID) that matches the same observed sequence will be aggregated.
 
 The aggregation of obsevered and expected IDs and abundances based on perfect matches

nextflow.config

@@ -105,6 +105,7 @@ params {
     // Comparison to expected
     expected_sequences                        = null
     expected_sequences_region                 = "query"
+    expected_sequences_mismatches             = 0
     expected_abundances                       = null
 
     // Report options

nextflow_schema.json

@@ -987,6 +987,14 @@
                     "default": "query",
                     "enum": ["alignment", "query", "target"]
                 },
+                "expected_sequences_mismatches": {
+                    "type": "integer",
+                    "default": 0,
+                    "minimum": 0,
+                    "description": "Threshold of accepted mismatches and gaps to the expected sequences",
+                    "help_text": "The number of mismatches and gaps that is accepted in the region avaluated by `--expected_sequences_region` to call it a match. For example, `0` means an exact match, 1 allows one mismatch/gap.",
+                    "fa_icon": "fas fa-greater-than-equal"
+                },
                 "expected_abundances": {
                     "type": "string",
                     "format": "file-path",