Merge branch 'CW-3200' into 'dev'

Increase default number of reads in pre-medaka downsampling [CW-3200] See merge request epi2melabs/workflows/wf-amplicon!56
epi2me-labs · Dec 15, 2023 · fadd19d · fadd19d
2 parents a4e8154 + 9afb157
commit fadd19d
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,7 +6,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [v1.0.1]
 ### Changed
-- Default for `--reads_downsampling_size` to 1500.
+- Default for `--reads_downsampling_size` to 1500 to limit memory usage.
+- Default for `--medaka_target_depth_per_strand` to 150 as the workflow now supports longer amplicons.
 
 ### Fixed
 - The workflow failing when a sample had only a single read.

diff --git a/README.md b/README.md
@@ -164,7 +164,7 @@ Find related protocols in the [Nanopore community](https://community.nanoporetec
 | Nextflow parameter name  | Type | Description | Help | Default |
 |--------------------------|------|-------------|------|---------|
 | number_depth_windows | integer | Number of windows used during depth of coverage calculations. | Depth of coverage is calculated for each sample across each amplicon split into this number of windows. A higher number will produce more fine-grained plots at the expense of run time. | 100 |
-| medaka_target_depth_per_strand | integer | Downsample each amplicon to this per-strand depth before running Medaka. | Medaka performs best with even strand coverage and depths between 80X and 400X. To avoid too high coverage, the workflow downsamples the reads for each amplicon to this per-strand depth before running Medaka. Changing this value is discouraged as it might cause decreased performance. | 75 |
+| medaka_target_depth_per_strand | integer | Downsample each amplicon to this per-strand depth before running Medaka. | Medaka performs best with even strand coverage and depths between 80X and 400X. To avoid too high coverage, the workflow downsamples the reads for each amplicon to this per-strand depth before running Medaka. Changing this value is discouraged as it might cause decreased performance. | 150 |
 
 
 ### Miscellaneous Options

diff --git a/docs/06_inputs.md b/docs/06_inputs.md
@@ -60,7 +60,7 @@
 | Nextflow parameter name  | Type | Description | Help | Default |
 |--------------------------|------|-------------|------|---------|
 | number_depth_windows | integer | Number of windows used during depth of coverage calculations. | Depth of coverage is calculated for each sample across each amplicon split into this number of windows. A higher number will produce more fine-grained plots at the expense of run time. | 100 |
-| medaka_target_depth_per_strand | integer | Downsample each amplicon to this per-strand depth before running Medaka. | Medaka performs best with even strand coverage and depths between 80X and 400X. To avoid too high coverage, the workflow downsamples the reads for each amplicon to this per-strand depth before running Medaka. Changing this value is discouraged as it might cause decreased performance. | 75 |
+| medaka_target_depth_per_strand | integer | Downsample each amplicon to this per-strand depth before running Medaka. | Medaka performs best with even strand coverage and depths between 80X and 400X. To avoid too high coverage, the workflow downsamples the reads for each amplicon to this per-strand depth before running Medaka. Changing this value is discouraged as it might cause decreased performance. | 150 |
 
 
 ### Miscellaneous Options

diff --git a/nextflow.config b/nextflow.config
@@ -34,7 +34,7 @@ params {
     min_coverage = 20
     basecaller_cfg = "[email protected]"
     medaka_model = null
-    medaka_target_depth_per_strand = 75
+    medaka_target_depth_per_strand = 150
 
     // de-novo mode options
     force_spoa_length_threshold = 2000

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -229,7 +229,7 @@
                 },
                 "medaka_target_depth_per_strand": {
                     "type": "integer",
-                    "default": 75,
+                    "default": 150,
                     "description": "Downsample each amplicon to this per-strand depth before running Medaka.",
                     "help_text": "Medaka performs best with even strand coverage and depths between 80X and 400X. To avoid too high coverage, the workflow downsamples the reads for each amplicon to this per-strand depth before running Medaka. Changing this value is discouraged as it might cause decreased performance."
                 }