expose -w piscem workdir parameter for simpleaf index

src/simpleaf_commands.rs

@@ -409,6 +409,16 @@ pub struct IndexOpts {
     )]
     pub hash_seed: u64,
 
+    /// working directory where temporary files should be placed
+    #[arg(
+        long = "work-dir",
+        conflicts_with = "use_piscem",
+        help_heading = "Piscem Index Options",
+        default_value = "./workdir.noindex",
+        display_order = 5
+    )]
+    pub work_dir: PathBuf,
+
     /// path to output directory (will be created if it doesn't exist)
     #[arg(short, long, display_order = 1)]
     pub output: PathBuf,

src/simpleaf_commands/indexing.rs

@@ -196,7 +196,9 @@ pub fn build_ref_and_index(af_home_path: &Path, opts: IndexOpts) -> anyhow::Resu
             .arg("-s")
             .arg(&ref_seq)
             .arg("--seed")
-            .arg(opts.hash_seed.to_string());
+            .arg(opts.hash_seed.to_string())
+            .arg("-w")
+            .arg(opts.work_dir);
 
         // if the user requested to overwrite, then pass this option
         if opts.overwrite {

src/utils/workflow_utils.rs

@@ -545,7 +545,7 @@ pub fn initialize_workflow<T: AsRef<Path>>(
 // Each SimpleafWorkflow represents a json
 /// Simpleaf Workflow record
 pub struct SimpleafWorkflow {
-    pub af_home_path: PathBuf,
+    // pub af_home_path: PathBuf,
 
     // This command queue contains all commands that need to be run
     pub cmd_queue: Vec<CommandRecord>,
@@ -995,7 +995,7 @@ impl WorkflowLog {
 /// It can be either a simpleaf command or an external command.
 pub struct CommandRecord {
     pub step: u64,
-    pub active: bool,
+    // pub active: bool,
     pub program_name: ProgramName,
     pub cmd: WFCommand,
     //pub simpleaf_cmd: Option<Commands>,