Merge pull request #22 from EBI-Metagenomics/filter_operator

Filter operator fix
EBI-Metagenomics · Nov 20, 2024 · 686fe47 · 686fe47
2 parents 36f9c8e + 8aa06e7
commit 686fe47
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Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/README.md b/README.md
@@ -221,7 +221,7 @@ SRR6180434,short_reads_filter_ratio_threshold_exceeded
 
 | Exclusion Message                 | Description                                                                                                                                                                                                                                                                            |
 | --------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `short_reads_filter_ratio_threshold_exceeded` | The maximum fraction of reads that are allowed to be filtered out. If exceeded, it flags excessive filtering. The default value is 0.9, meaning that if more than 90% of the reads are filtered out, the threshold is considered exceeded, and the run is not assembled. |
+| `short_reads_filter_ratio_threshold_exceeded` | The maximum fraction of reads that are allowed to be filtered out. If exceeded, it flags excessive filtering. The default value is 0.1, meaning that if less than 10% of the reads are retained after filtering, the threshold is considered exceeded, and the run is not assembled. |
 | `short_reads_low_reads_count_threshold`       | The minimum number of reads required after filtering. If below, it flags a low read count, and the run is not assembled.                                                                                                                                                               |
 
 #### Assembled Runs

diff --git a/nextflow.config b/nextflow.config
@@ -32,7 +32,7 @@ params {
     // QC FILTERING
 
     // Short reads QC filtering options
-    short_reads_filter_ratio_threshold    = 0.9
+    short_reads_filter_ratio_threshold    = 0.1
     short_reads_low_reads_count_threshold = 1000
 
     // Long reads options

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -194,8 +194,8 @@
             "properties": {
                 "short_reads_filter_ratio_threshold": {
                     "type": "number",
-                    "description": "The maximum fraction of reads that are allowed to be filtered out. If exceeded, it flags excessive filtering. The default value is 0.9, meaning that if more than 90% of the reads are filtered out, the threshold is considered exceeded, and the run is not assembled.",
-                    "default": 0.9,
+                    "description": "The maximum fraction of reads that are allowed to be filtered out. If exceeded, it flags excessive filtering. The default value is 0.1, meaning that if less than 10% of the reads are retained after filtering, the threshold is considered exceeded, and the run is not assembled.",
+                    "default": 0.1,
                     "minimum": 0.0,
                     "maximum": 1.0
                 },

diff --git a/workflows/short_reads_assembler.nf b/workflows/short_reads_assembler.nf
@@ -94,7 +94,7 @@ workflow SHORT_READS_ASSEMBLER {
 
     /******************************************/
     /*  Reads that fail the following rules:  */
-    /*  - Reads discarded by fastp > 90% (default value) */
+    /*  - Reads kept by fastp < 10% (default value) */
     /*  - Less than 1k reads                  */
     /******************************************/
     extended_qc = SHORT_READS_QC.out.fastp_json.map { meta, json -> {