ENH Add __extra_megahit_args to assemble()

Allow users to directly pass arguments to megahit closes #86
ngless-toolkit · Oct 28, 2018 · 71d8af1 · 71d8af1
1 parent 8af2ec8
commit 71d8af1
Show file tree

Hide file tree

Showing 3 changed files with 18 additions and 4 deletions.
diff --git a/ChangeLog b/ChangeLog
@@ -8,6 +8,7 @@ Version 0.9.1+
 	* arg1 in external modules is no longer always treated as a path
 	* Added expand_searchdir to external modules API (closes #56)
 	* Fix saving fastq sets with --subsample (issue #85)
+	* Add __extra_megahit_args to assemble() (issue #86)
 
 Version 0.9.1 2018-07-17 by luispedro
 	* Add biorxiv citation

diff --git a/NGLess/BuiltinModules/Assemble.hs b/NGLess/BuiltinModules/Assemble.hs
@@ -1,4 +1,4 @@
-{- Copyright 2017 NGLess Authors
+{- Copyright 2017-2018 NGLess Authors
  - License: MIT
  -}
 
@@ -27,7 +27,7 @@ import Utils.Utils (readProcessErrorWithExitCode)
 
 
 executeAssemble :: T.Text -> NGLessObject -> KwArgsValues -> NGLessIO NGLessObject
-executeAssemble "assemble" expr [] = do
+executeAssemble "assemble" expr kwargs = do
     files <- case expr of
             NGOReadSet _ (ReadSet [] singles) -> do
                 FastQFilePath _ f <- concatenateFQs singles
@@ -45,14 +45,15 @@ executeAssemble "assemble" expr [] = do
     megahitPath <- megahitBin
     keepTempFiles <- nConfKeepTemporaryFiles <$> nglConfiguration
     nthreads <- liftIO getNumCapabilities
+    extraArgs <- map T.unpack <$> lookupStringListOrScriptErrorDef (return []) "extra megahit arguments" "__extra_megahit_args" kwargs
     (_, tdir) <- createTempDir "ngless-megahit-assembly"
     (_, mhtmpdir) <- createTempDir "ngless-megahit-tmpdir"
     let odir = tdir </> "megahit-output"
         args = files ++
                         ["-o", odir
                         ,"--num-cpu-threads", show nthreads
                         ,"--tmp-dir", mhtmpdir
-                        ] ++ ["--keep-tmp-files" | keepTempFiles]
+                        ] ++ ["--keep-tmp-files" | keepTempFiles] ++ extraArgs
     outputListLno' DebugOutput ["Calling megahit: ", megahitPath, " ", unwords args]
     (errmsg, exitCode) <- liftIO $ readProcessErrorWithExitCode
                                     (proc megahitPath args)
@@ -69,7 +70,7 @@ assembleFunction = Function
     , funcArgType = Just NGLReadSet
     , funcArgChecks = []
     , funcRetType = NGLString
-    , funcKwArgs = []
+    , funcKwArgs = [ArgInformation "__extra_megahit_args" False (NGList NGLString) []]
     , funcAllowsAutoComprehension = False
     , funcChecks = [FunctionCheckReturnAssigned]
     }

diff --git a/docs/sources/Functions.rst b/docs/sources/Functions.rst
@@ -645,6 +645,18 @@ Returns
 
 string : generated file
 
+Arguments by value:
+~~~~~~~~~~~~~~~~~~~
+
++-----------------------+-------------+------------+----------------+
+| Name                  | Type        | Required   | Default Value  |
++=======================+=============+============+================+
+| __extra_megahit_arg   | List of str | no         | []             |
++-----------------------+-------------+------------+----------------+
+
+``__extra_megahit_arg`` is passed directly to megahit with no checking.
+
+
 orf_find
 --------