[Add] monkeypox config + resources

cbg-ethz · Mar 16, 2023 · a6a9c9c · a6a9c9c
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diff --git a/config/mpxv.yaml b/config/mpxv.yaml
@@ -0,0 +1,28 @@
+---
+name: MPXV
+
+general:
+    aligner: bwa
+    primers_trimmer: samtools
+    snv_caller: lofreq
+
+input:
+    reference: "{VPIPE_BASEDIR}/../resources/mpxv/MT903345.1.fasta"
+    primers_file: "{VPIPE_BASEDIR}/../resources/mpxv/primers/MPXV-primer_genome-positions_subset.tsv"
+    primers_bedfile: "{VPIPE_BASEDIR}/../resources/mpxv/primers/MPXV-primer_genome-positions_subset.bed"
+    datadir: "{VPIPE_BASEDIR}/../resources/samples/"
+    samples_file: samples.tsv
+
+snv:
+    consensus: false
+
+preprocessing:
+    extra: -ns_max_n 4 -min_qual_mean 20 -trim_qual_left 20 -trim_qual_right 20 -trim_qual_window 10
+
+output:
+    trim_primers: true
+    snv: true
+    local: true
+    global: false
+    visualization: true
+    QA: true