reintroduce --min-sequence-length paraameter

alpae · alpae · commit 1d85604a8b6c · 2025-10-07T15:48:55.000+02:00
set default to 20 AA.
diff --git a/FastOMA.nf b/FastOMA.nf
@@ -237,6 +237,7 @@ process infer_roothogs{
                                --hogmap hogmaps \
                                --splice ${splice_folder} \
                                --out-rhog-folder "omamer_rhogs" \
+                               --min-sequence-length ${params.min_sequence_length} \
                                -vv
     """
 }
diff --git a/nextflow.config b/nextflow.config
@@ -24,7 +24,7 @@ params {
   filter_gap_ratio_row = 0.3
   filter_gap_ratio_col = 0.5
   nr_repr_per_hog = 5
-  min_sequence_length = 40
+  min_sequence_length = 20
   force_pairwise_ortholog_generation = false
 
   output_folder = "Output"

Original file line number	Diff line number	Diff line change
`@@ -237,6 +237,7 @@ process infer_roothogs{`
`237`	`237`	`--hogmap hogmaps \`
`238`	`238`	`--splice ${splice_folder} \`
`239`	`239`	`--out-rhog-folder "omamer_rhogs" \`
	`240`	`+ --min-sequence-length ${params.min_sequence_length} \`
`240`	`241`	`-vv`
`241`	`242`	`"""`
`242`	`243`	`}`