The version of the ProtQC package is not matched.

resources/quartet-protqc-report/bin/protqc.sh

@@ -29,7 +29,7 @@ EOF
 
 while getopts ":hd:m:o:" arg; do
 	case "$arg" in
-	"e")
+	"d")
 		DATA_FILE="$OPTARG"
 		;;
 	"m")

resources/renv.lock

@@ -48,15 +48,15 @@
     },
     "ProtQC": {
       "Package": "ProtQC",
-      "Version": "0.1.0",
+      "Version": "0.1.3",
       "Source": "GitHub",
       "RemoteType": "github",
       "RemoteHost": "api.github.com",
       "RemoteRepo": "ProtQC",
       "RemoteUsername": "chinese-quartet",
-      "RemoteRef": "v0.1.2",
-      "RemoteSha": "22fbe4ad61d183530f737335d7c730de876d85bc",
-      "Hash": "6ce010c606427ed07ea8f8925577564c"
+      "RemoteRef": "v0.1.3",
+      "RemoteSha": "01edb13db10e24e38aa06299bfe7b69e009cd134",
+      "Hash": "c5ae657d64a2afd72770effa4767a049"
     },
     "R6": {
       "Package": "R6",

resources/tservice-plugin.yaml

@@ -19,6 +19,7 @@ init:
   # Unpack environment file to the directory, repository/envs/quartet-protqc-report
   - step: unpack-env
     envname: quartet-protqc-report
+    postunpack: chmod a+x {{ENV_DEST_DIR}}/quartet-protqc-report/bin/protqc.sh
   - step: load-namespace
     namespace: tservice.plugins.quartet-protqc-report
   - step: register-plugin

src/tservice/plugins/quartet_protqc_report.clj

@@ -4,7 +4,7 @@
             [spec-tools.core :as st]
             [clojure.tools.logging :as log]
             [tservice.lib.files :as ff]
-            [tservice.api.storage.fs :as fs-api]
+            [clojure.string :as clj-str]
             [tservice.lib.fs :as fs-lib]
             [tservice.vendor.multiqc :as mq]
             [tservice.plugins.quartet-protqc-report.protqc :as protqc]
@@ -60,7 +60,7 @@
                (let [payload (merge {:description description} payload)
                      data-file (protqc/correct-filepath data_file)
                      metadata-file (protqc/correct-filepath metadata_file)
-                     workdir (fs-api/dirname data-file)
+                     workdir (protqc/dirname data-file)
                      log-path (fs-lib/join-paths workdir "log")
                      response {:report (format "%s/multireport.html" workdir)
                                :log log-path
@@ -74,7 +74,7 @@
                                             :response       response})
                      result-dir (fs-lib/join-paths workdir "results")]
                  (fs-lib/create-directories! result-dir)
-                 (log/info (format "Create a report %s with %s" name payload))
+                 (log/info (format "Create a report %s with %s in %s" name payload workdir))
                  (spit log-path (json/write-str {:status "Running"
                                                  :msg ""}))
                  (update-process! task-id 0)

src/tservice/plugins/quartet_protqc_report/protqc.clj

@@ -3,7 +3,8 @@
   (:require [tservice.api.config :refer [add-env-to-path]]
             [tservice.lib.files :refer [is-localpath?]]
             [clojure.string :as clj-str]
-            [clojure.java.shell :as shell :refer [sh]]))
+            [clojure.java.shell :as shell :refer [sh]]
+            [clojure.java.io :refer [file]]))
 
 (defn call-protqc!
   "Call protqc bash script. more details on https://github.com/chinese-quartet/ProtQC
@@ -28,3 +29,24 @@
   (if (is-localpath? filepath)
     (clj-str/replace filepath #"^file:\/\/" "")
     filepath))
+
+(defn ^String basename
+  "Returns the basename of 'path'.
+   This works by calling getName() on a java.io.File instance. It's prefered
+   over last-dir-in-path for that reason.
+   Parameters:
+     path - String containing the path for an item in iRODS.
+   Returns:
+     String containing the basename of path."
+  [^String path]
+  (.getName (file path)))
+
+(defn ^String dirname
+  "Returns the dirname of 'path'.
+   This works by calling getParent() on a java.io.File instance.
+   Parameters:
+     path - String containing the path for an item in iRODS.
+   Returns:
+     String containing the dirname of path."
+  [^String path]
+  (when path (.getParent (file path))))