From f500b64eed3d819d994487a512175dda783744f1 Mon Sep 17 00:00:00 2001
From: Lucas Taniguti <lucas.biotec07@gmail.com>
Date: Sun, 17 Dec 2023 22:28:37 -0300
Subject: [PATCH] =?UTF-8?q?=E2=9C=A8=20Add=20HAPPY=20task=20and=20test=20f?=
 =?UTF-8?q?iles?=
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---
 tasks/happy/happy.wdl                        | 69 ++++++++++++++++++++
 tests/tasks/happy/happy/inputs.json          |  9 +++
 tests/tasks/happy/happy/run.sh               |  5 ++
 tests/tasks/happy/happy/test_happy_task.yaml | 28 ++++++++
 4 files changed, 111 insertions(+)
 create mode 100644 tasks/happy/happy.wdl
 create mode 100644 tests/tasks/happy/happy/inputs.json
 create mode 100644 tests/tasks/happy/happy/run.sh
 create mode 100644 tests/tasks/happy/happy/test_happy_task.yaml

diff --git a/tasks/happy/happy.wdl b/tasks/happy/happy.wdl
new file mode 100644
index 0000000..2f75cb6
--- /dev/null
+++ b/tasks/happy/happy.wdl
@@ -0,0 +1,69 @@
+version 1.0
+
+task HAPPY {
+    input {
+        File truth_vcf
+        File query_vcf
+        String prefix
+        File fasta
+        File fasta_fai
+        File? regions_bed
+        File? targets_bed
+        File? false_positives_bed
+        File? stratification_tsv
+
+        Int cpus
+        Boolean stub = false
+    }
+
+
+    command <<<
+        hap.py -v > version.txt  # It's not working as expected. Just prints Hap.py
+
+        if [ ~{stub} == "true" ]; then
+            touch ~{prefix}.summary.csv \
+                  ~{prefix}.roc.all.csv.gz \
+                  ~{prefix}.roc.Locations.INDEL.csv.gz \
+                  ~{prefix}.roc.Locations.INDEL.PASS.csv.gz \
+                  ~{prefix}.roc.Locations.SNP.csv.gz \
+                  ~{prefix}.roc.Locations.SNP.PASS.csv.gz \
+                  ~{prefix}.extended.csv \
+                  ~{prefix}.runinfo.json \
+                  ~{prefix}.metrics.json.gz \
+                  ~{prefix}.vcf.gz \
+                  ~{prefix}.vcf.gz.tbi
+            exit 0
+        fi
+
+        hap.py \
+            ~{truth_vcf} \
+            ~{query_vcf} \
+            ~{"--reference " + fasta} \
+            ~{"--threads " + cpus} \
+            ~{"--R " + regions_bed } \
+            ~{"--T " + targets_bed } \
+            ~{"--false-positives " + false_positives_bed} \
+            ~{"--stratification " + stratification_tsv} \
+            -o ~{prefix}
+    >>>
+
+    output {
+        File summary_csv = "~{prefix}.summary.csv"
+        File roc_all_csv = "~{prefix}.roc.all.csv.gz"
+        File roc_indel_locations_csv = "~{prefix}.roc.Locations.INDEL.csv.gz"
+        File roc_indel_locations_pass_csv = "~{prefix}.roc.Locations.INDEL.PASS.csv.gz"
+        File roc_snp_locations_csv = "~{prefix}.roc.Locations.SNP.csv.gz"
+        File roc_snp_locations_pass_csv = "~{prefix}.roc.Locations.SNP.PASS.csv.gz"
+        File extended_csv = "~{prefix}.extended.csv"
+        File runinfo = "~{prefix}.runinfo.json"
+        File metrics_json = "~{prefix}.metrics.json.gz"
+        File vcf = "~{prefix}.vcf.gz"
+        File tbi = "~{prefix}.vcf.gz.tbi"
+        File version = "version.txt"
+    }
+
+    runtime {
+        docker: "quay.io/biocontainers/hap.py:0.3.14--py27h5c5a3ab_0"
+        cpu: cpus
+    }
+}
diff --git a/tests/tasks/happy/happy/inputs.json b/tests/tasks/happy/happy/inputs.json
new file mode 100644
index 0000000..57d3577
--- /dev/null
+++ b/tests/tasks/happy/happy/inputs.json
@@ -0,0 +1,9 @@
+{
+    "truth_vcf": "truth.vcf.gz",
+    "query_vcf": "query.vcf.gz",
+    "prefix": "benchmark-outputs",
+    "fasta": "reference.fasta",
+    "fasta_fai": "reference.fasta.fai",
+    "cpus": 4,
+    "stub": true
+}
diff --git a/tests/tasks/happy/happy/run.sh b/tests/tasks/happy/happy/run.sh
new file mode 100644
index 0000000..d744a49
--- /dev/null
+++ b/tests/tasks/happy/happy/run.sh
@@ -0,0 +1,5 @@
+set -e
+
+touch truth.vcf.gz query.vcf.gz reference.fasta reference.fasta.fai
+
+miniwdl run --task HAPPY -i tests/tasks/happy/happy/inputs.json tasks/happy/happy.wdl
diff --git a/tests/tasks/happy/happy/test_happy_task.yaml b/tests/tasks/happy/happy/test_happy_task.yaml
new file mode 100644
index 0000000..6cd1009
--- /dev/null
+++ b/tests/tasks/happy/happy/test_happy_task.yaml
@@ -0,0 +1,28 @@
+- name: Check if HAPPY produces the expected outputs
+  tags:
+  - happy/happy
+  command: bash tests/tasks/happy/happy/run.sh
+  files:
+  - path: _LAST/out/summary_csv/benchmark-outputs.summary.csv
+  - path: _LAST/out/roc_all_csv/benchmark-outputs.roc.all.csv.gz
+  - path: _LAST/out/roc_indel_locations_csv/benchmark-outputs.roc.Locations.INDEL.csv.gz
+  - path: _LAST/out/roc_indel_locations_pass_csv/benchmark-outputs.roc.Locations.INDEL.PASS.csv.gz
+  - path: _LAST/out/roc_snp_locations_csv/benchmark-outputs.roc.Locations.SNP.csv.gz
+  - path: _LAST/out/roc_snp_locations_pass_csv/benchmark-outputs.roc.Locations.SNP.PASS.csv.gz
+  - path: _LAST/out/extended_csv/benchmark-outputs.extended.csv
+  - path: _LAST/out/runinfo/benchmark-outputs.runinfo.json
+  - path: _LAST/out/metrics_json/benchmark-outputs.metrics.json.gz
+  - path: _LAST/out/vcf/benchmark-outputs.vcf.gz
+  - path: _LAST/out/tbi/benchmark-outputs.vcf.gz.tbi
+  - path: _LAST/out/version/version.txt
+    contains:
+    - "Hap.py"
+  - path: _LAST/command
+    contains:
+    - "hap.py \\"
+    - "-o benchmark-outputs"
+    - "--threads 4"
+    contains_regex:
+    - "--reference .+\\/reference.fasta"
+    - ".+\\/truth.vcf.gz"
+    - ".+\\/query.vcf.gz"