From 9a3cf9f6230db9a453f06d72c8cb9fba9fe8bbc4 Mon Sep 17 00:00:00 2001 From: Jennifer Mattock Date: Wed, 20 Nov 2024 15:05:08 +0000 Subject: [PATCH 1/2] amended filter ratio threshold to 10% --- README.md | 2 +- nextflow.config | 2 +- workflows/short_reads_assembler.nf | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 2d15f73..037c9eb 100644 --- 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 index e89c6d5..52f1cd3 100644 --- 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/workflows/short_reads_assembler.nf b/workflows/short_reads_assembler.nf index f159e84..e38a676 100644 --- 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 -> { From 8aa06e74108adaad241fffb9dfe1e5dadba12ef8 Mon Sep 17 00:00:00 2001 From: jmattock5 <80533767+jmattock5@users.noreply.github.com> Date: Wed, 20 Nov 2024 16:19:11 +0000 Subject: [PATCH 2/2] Update nextflow_schema.json Changed ratio threshold default to 0.1 and amended description --- nextflow_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index da9c14b..f3e69d7 100644 --- 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 },