remove excess optimOTU Docker options

Author: METS0JA

src/components/Run.vue

@@ -913,7 +913,6 @@ export default {
               Tty: false,
               AttachStdout: true,
               AttachStderr: true,
-              Platform: "linux/amd64",
               Env: [
                 `HOST_UID=${this.userId}`,
                 `HOST_GID=${this.groupId}`,
@@ -922,10 +921,6 @@ export default {
                 `fileFormat=${this.$store.state.data.fileFormat}`,
                 `readType=${this.$store.state.data.readType}`,
                 `readType=${this.$store.state.data.readType}`,
-                'R_ENABLE_JIT=0',                    // Disable JIT compilation
-                'R_COMPILE_PKGS=0',                  // Disable package compilation
-                'R_DISABLE_BYTECODE=1',              // Disable bytecode compilation
-                'R_KEEP_PKG_SOURCE=yes'              // Keep package sources
               ],
               HostConfig: {
                 Binds: this.getOptimOTUBinds(),

src/pipecraft-core/service_scripts/pipeline_options.yaml

@@ -14,8 +14,8 @@ trimming:
   min_overlap: 10
   max_n: 0
   max_err: 1
-  truncQ_R1: 3
-  truncQ_R2: 3
+  truncQ_R1: 2
+  truncQ_R2: 2
   min_length: 100
   cut_R1: 0
   cut_R2: 0
@@ -35,7 +35,7 @@ orient: fwd
 control:
   spike:
   positive:
-forward_primer: "GCATCGATGAAGAACGCAGC"
+forward_primer: "GTGARTCATCGAATCTTTG"
 reverse_primer: "TCCTCCGCTTATTGATATGC"
 custom_sample_table: FALSE
 filtering:
@@ -48,7 +48,6 @@ amplicon_model:
   model_type: CM
   model_file: /optimotu_targets/data/ITS3_ITS4.cm
   model_align: no
-  numt_filter: no
   model_filter:
     max_model_start: 5
     min_model_end: 140