feat: implement more of the sprocket run command.

Cargo.toml

@@ -38,5 +38,7 @@ tracing = "0.1.40"
 tracing-subscriber = { version = "0.3.18", features = ["env-filter"] }
 url = "2.5.2"
 wdl-analysis = { git = "https://github.com/peterhuene/wdl", branch = "hackathon" }
-wdl-ast = { git = "https://github.com/peterhuene/wdl", branch = "hackathon" }
-wdl-grammar = { git = "https://github.com/peterhuene/wdl", branch = "hackathon" }
+wdl-ast = { git = "https://github.com/peterhuene/wdl", branch = "hackathon", features = ["codespan"] }
+wdl-grammar = { git = "https://github.com/peterhuene/wdl", branch = "hackathon", features = ["codespan"] }
+codespan-reporting = "0.11.1"
+colored = "2.1.0"

crankshaft/Cargo.toml

@@ -6,6 +6,7 @@ edition = "2021"
 [dependencies]
 indicatif = { workspace = true }
 tes = { path = "../tes", version = "0.1.0" }
+wdl-runtime = { path = "../wdl-runtime", version = "0.1.0" }
 async-trait = { workspace = true }
 bollard = { workspace = true }
 bytes = { workspace = true }
@@ -34,6 +35,8 @@ wdl-ast = { workspace = true }
 wdl-analysis = { workspace = true }
 anyhow = { workspace = true }
 tar.workspace = true
+codespan-reporting = { workspace = true }
+colored = { workspace = true }
 
 [lints.rust]
 missing_docs = "warn"

crankshaft/demo.json

@@ -0,0 +1,3 @@
+{
+    "url": "https://www.encodeproject.org/files/ENCFF863PGO/@@download/ENCFF863PGO.bam"
+}

crankshaft/demo.wdl

@@ -0,0 +1,21 @@
+## This is a demonstration of evaluating WDL and running a task using crankshaft.
+
+version 1.2
+
+task samtools_flagstat {
+    input {
+        String url
+    }
+
+    command <<<
+        samtools flagstat <(wget -O - -q '~{url}' | samtools view -h | head -n 100000)
+    >>>
+
+    requirements {
+        container: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_0"
+    }
+
+    output {
+        String stats = read_string(stdout())
+    }
+}