diff --git a/resources/report-table-formatter.js b/resources/report-table-formatter.js
deleted file mode 100644
index 8104024d..00000000
--- a/resources/report-table-formatter.js
+++ /dev/null
@@ -1,59 +0,0 @@
-{
- "breakpoint_seq": function format(value) {
- var primer_blast_url = `https://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?LINK_LOC=bookmark&INPUT_SEQUENCE=${value}&PRIMER5_END=900&PRIMER3_START=1100&PRIMER_PRODUCT_MIN=200&PRIMER_PRODUCT_MAX=1200&ORGANISM=Homo%20sapiens&NEWWIN=on&NEWWIN=on&SHOW_SVIEWER=true`;
- var seq = "…" + value.substring(value.length / 2 - 10, value.length / 2 + 10) + "…";
- var link = `${seq}`;
- return link;
- },
- "EVENT": function format(value) {
- var filename = value.replace("_circle_", "_");
- var link = `${value}`;
- return link;
- },
- "GENES": function format(value) {
- $(function () {
- $('[data-toggle="tooltip"]').tooltip()
- });
- let genes = value.split(";");
- let rows = "";
- for (let g of genes) {
- rows = `${rows}
${g} |
`;
- };
- let table = ``;
- let button = ``;
- return button;
- },
- "gene_helper": function format(value) {
- $(function () {
- $('[data-toggle="tooltip"]').tooltip()
- });
- let genes = value.split(";");
- let rows = "";
- for (let g of genes) {
- rows = `${rows}${g} |
`;
- };
- let table = ``;
- let button = ``;
- return button;
- },
- "GENES": function format(value) {
- return this["gene_helper"](value);
- },
- "GENES_1": function format(value) {
- return this["gene_helper"](value);
- },
- "GENES_2": function format(value) {
- return this["gene_helper"](value);
- },
- "GENES_3": function format(value) {
- return this["gene_helper"](value);
- },
- "GENES_4": function format(value) {
- return this["gene_helper"](value);
- },
-}
-
diff --git a/resources/scenarios/illumina_circle_scenario.yaml b/workflow/resources/scenarios/illumina_circle_scenario.yaml
similarity index 100%
rename from resources/scenarios/illumina_circle_scenario.yaml
rename to workflow/resources/scenarios/illumina_circle_scenario.yaml
diff --git a/resources/scenarios/nanopore_circle_scenario.yaml b/workflow/resources/scenarios/nanopore_circle_scenario.yaml
similarity index 100%
rename from resources/scenarios/nanopore_circle_scenario.yaml
rename to workflow/resources/scenarios/nanopore_circle_scenario.yaml
diff --git a/resources/scenarios/nanopore_illumina_joint_circle_scenario.yaml b/workflow/resources/scenarios/nanopore_illumina_joint_circle_scenario.yaml
similarity index 100%
rename from resources/scenarios/nanopore_illumina_joint_circle_scenario.yaml
rename to workflow/resources/scenarios/nanopore_illumina_joint_circle_scenario.yaml
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index 2c32dcde..5ba61120 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -175,11 +175,17 @@ def scenario_name(wildcards):
def get_scenario(wildcards):
scenario = scenario_name(wildcards)
if scenario == "nanopore_only":
- return "resources/scenarios/nanopore_circle_scenario.yaml"
+ return workflow.source_path(
+ "../resources/scenarios/nanopore_circle_scenario.yaml"
+ )
elif scenario == "illumina_only":
- return "resources/scenarios/illumina_circle_scenario.yaml"
+ return workflow.source_path(
+ "../resources/scenarios/illumina_circle_scenario.yaml"
+ )
elif scenario == "nanopore_with_illumina_support":
- return "resources/scenarios/nanopore_illumina_joint_circle_scenario.yaml"
+ return workflow.source_path(
+ "../resources/scenarios/nanopore_illumina_joint_circle_scenario.yaml"
+ )
else:
raise ValueError(f"Unknown scenario: {scenario}")