fix typos spotted across docs (#205)

Co-authored-by: Michael R. Crusoe <[email protected]>

Author: fmigneault

CommandLineTool.yml

@@ -104,7 +104,7 @@ $graph:
       where these approaches are application or platform specific it creates a
       significant barrier to reproducibility and portability, as methods
       developed for one platform must be manually ported to be used on new
-      platforms.  Similarly it creates redundant work, as wrappers for popular
+      platforms.  Similarly, it creates redundant work, as wrappers for popular
       tools must be rewritten for each application or platform in use.
 
       The Common Workflow Language Command Line Tool Description is designed to
@@ -143,7 +143,7 @@ $graph:
   doc: |
 
     When listed under `inputBinding` in the input schema, the term
-    "value" refers to the the corresponding value in the input object.  For
+    "value" refers to the corresponding value in the input object.  For
     binding objects listed in `CommandLineTool.arguments`, the term "value"
     refers to the effective value after evaluating `valueFrom`.
 
@@ -168,7 +168,7 @@ $graph:
 
       - **array**: If `itemSeparator` is specified, add `prefix` and the join
           the array into a single string with `itemSeparator` separating the
-          items.  Otherwise first add `prefix`, then recursively process
+          items.  Otherwise, first add `prefix`, then recursively process
           individual elements.
           If the array is empty, it does not add anything to command line.
 
@@ -203,7 +203,7 @@ $graph:
       type: string?
       doc: |
         Join the array elements into a single string with the elements
-        separated by by `itemSeparator`.
+        separated by `itemSeparator`.
     - name: valueFrom
       type:
         - "null"
@@ -310,7 +310,7 @@ $graph:
         element.  The exit code of the process is
         available in the expression as `runtime.exitCode`.
 
-        Additionally if `loadContents` is true, the file must be a
+        Additionally, if `loadContents` is true, the file must be a
         UTF-8 text file 64 KiB or smaller, and the implementation must
         read the entire contents of the file (or file array) and place
         it in the `contents` field of the File object for use in
@@ -457,7 +457,7 @@ $graph:
     - name: inputBinding
       type: CommandLineBinding?
       doc: |
-        Describes how to turns the input parameters of a process into
+        Describes how to turn the input parameters of a process into
         command line arguments.
       jsonldPredicate: "cwl:inputBinding"
 
@@ -745,7 +745,7 @@ $graph:
   extends: ProcessRequirement
   doc: |
     Indicates that a workflow component should be run in a
-    [Docker](http://docker.com) or Docker-compatible (such as
+    [Docker](https://docker.com) or Docker-compatible (such as
     [Singularity](https://www.sylabs.io/) and [udocker](https://github.com/indigo-dc/udocker)) container environment and
     specifies how to fetch or build the image.
 
@@ -815,7 +815,7 @@ $graph:
         `dockerPull: ubuntu@sha256:45b23dee08af5e43a7fea6c4cf9c25ccf269ee113168c19722f87876677c5cb2`
     - name: dockerLoad
       type: string?
-      doc: "Specify a HTTP URL from which to download a Docker image using `docker load`."
+      doc: "Specify an HTTP URL from which to download a Docker image using `docker load`."
     - name: dockerFile
       type: string?
       doc: "Supply the contents of a Dockerfile which will be built using `docker build`."
@@ -881,7 +881,7 @@ $graph:
         One or more [IRI](https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier)s
         identifying resources for installing or enabling the software named in
         the `package` field. Implementations may provide resolvers which map
-        these software identifer IRIs to some configuration action; or they can
+        these software identifier IRIs to some configuration action; or they can
         use only the name from the `package` field on a best effort basis.
 
         For example, the IRI https://packages.debian.org/bowtie could
@@ -893,15 +893,15 @@ $graph:
         software installation or selection mechanism.
         Using [RRID](https://www.identifiers.org/rrid/) as an example:
         https://identifiers.org/rrid/RRID:SCR_005476
-        could be fulfilled using the above mentioned Debian or bioconda
-        package, a local installation managed by [Environment Modules](http://modules.sourceforge.net/),
+        could be fulfilled using the above-mentioned Debian or bioconda
+        package, a local installation managed by [Environment Modules](https://modules.sourceforge.net/),
         or any other mechanism the platform chooses. IRIs can also be from
-        identifer sources that are discipline specific yet still system
+        identifier sources that are discipline specific yet still system
         independent. As an example, the equivalent [ELIXIR Tools and Data
         Service Registry](https://bio.tools) IRI to the previous RRID example is
         https://bio.tools/tool/bowtie2/version/2.2.8.
         If supported by a given registry, implementations are encouraged to
-        query these system independent sofware identifier IRIs directly for
+        query these system independent software identifier IRIs directly for
         links to packaging systems.
 
         A site specific IRI can be listed as well. For example, an academic
@@ -1293,7 +1293,7 @@ $graph:
     For implementations that support reusing output from past work (on
     the assumption that same code and same input produce same
     results), control whether to enable or disable the reuse behavior
-    for a particular tool or step (to accomodate situations where that
+    for a particular tool or step (to accommodate situations where that
     assumption is incorrect).  A reused step is not executed but
     instead returns the same output as the original execution.
 
@@ -1332,7 +1332,7 @@ $graph:
     may apply their own security policies to restrict what is
     accessible by the tool.
 
-    Enabling network access does not imply a publically routable IP
+    Enabling network access does not imply a publicly routable IP
     address or the ability to accept inbound connections.
 
   fields:
@@ -1369,7 +1369,7 @@ $graph:
     read-only in every step.
 
     Workflow steps which modify a file must produce the modified file
-    as output.  Downstream steps which futher process the file must
+    as output.  Downstream steps which further process the file must
     use the output of previous steps, and not refer to a common input
     (this is necessary for both ordering and correctness).
 

Process.yml

@@ -82,7 +82,7 @@ $graph:
     If no `location` or `path` is specified, a file object must specify
     `contents` with the UTF-8 text content of the file.  This is a "file
     literal".  File literals do not correspond to external resources, but are
-    created on disk with `contents` with when needed for a executing a tool.
+    created on disk with `contents` with when needed for executing a tool.
     Where appropriate, expressions can return file literals to define new files
     on a runtime.  The maximum size of `contents` is 64 kilobytes.
 
@@ -168,7 +168,7 @@ $graph:
         executed.  This field must be set by the implementation.  The final
         path component must match the value of `basename`.  This field
         must not be used in any other context.  The command line tool being
-        executed must be able to to access the file at `path` using the POSIX
+        executed must be able to access the file at `path` using the POSIX
         `open(2)` syscall.
 
         As a special case, if the `path` field is provided but the `location`
@@ -216,7 +216,7 @@ $graph:
       doc: |
         The basename root such that `nameroot + nameext == basename`, and
         `nameext` is empty or begins with a period and contains at most one
-        period.  For the purposess of path splitting leading periods on the
+        period.  For the purposes of path splitting leading periods on the
         basename are ignored; a basename of `.cshrc` will have a nameroot of
         `.cshrc`.
 
@@ -235,7 +235,7 @@ $graph:
     - name: checksum
       type: string?
       doc: |
-        Optional hash code for validating file integrity.  Currently must be in the form
+        Optional hash code for validating file integrity.  Currently, must be in the form
         "sha1$ + hexadecimal string" using the SHA-1 algorithm.
     - name: size
       type:
@@ -266,7 +266,7 @@ $graph:
         identity: true
       doc: |
         The format of the file: this must be an IRI of a concept node that
-        represents the file format, preferrably defined within an ontology.
+        represents the file format, preferably defined within an ontology.
         If no ontology is available, file formats may be tested by exact match.
 
         Reasoning about format compatibility must be done by checking that an
@@ -289,7 +289,7 @@ $graph:
         `location` field.  When the file is staged as input to CommandLineTool,
         the value of `contents` must be written to a file.
 
-        If `contents` is set as a result of an Javascript expression,
+        If `contents` is set as a result of a Javascript expression,
         an `entry` in `InitialWorkDirRequirement`, or read in from
         `cwl.output.json`, there is no specified upper limit on the
         size of `contents`.  Implementations may have practical limits
@@ -392,7 +392,7 @@ $graph:
         The local path where the Directory is made available prior to executing a
         CommandLineTool.  This must be set by the implementation.  This field
         must not be used in any other context.  The command line tool being
-        executed must be able to to access the directory at `path` using the POSIX
+        executed must be able to access the directory at `path` using the POSIX
         `opendir(2)` syscall.
 
         If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)
@@ -591,7 +591,7 @@ $graph:
 
         This must be one or more IRIs of concept nodes
         that represents file formats which are allowed as input to this
-        parameter, preferrably defined within an ontology.  If no ontology is
+        parameter, preferably defined within an ontology.  If no ontology is
         available, file formats may be tested by exact match.
 
 
@@ -888,7 +888,7 @@ $graph:
         CommandLineTool, Workflow, or ExpressionTool.
 
         If provided, then this must be an IRI of a concept node that
-        represents the type of operation, preferrably defined within an ontology.
+        represents the type of operation, preferably defined within an ontology.
 
         For example, in the domain of bioinformatics, one can use an IRI from
         the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004),
@@ -903,7 +903,7 @@ $graph:
   doc: |
     Indicates that the workflow platform must support inline Javascript expressions.
     If this requirement is not present, the workflow platform must not perform expression
-    interpolatation.
+    interpolation.
   fields:
     - name: class
       type:

Workflow.yml

@@ -312,7 +312,7 @@ $graph:
     workflow inputs, or the outputs of other workflows steps) with the input
     parameters of the process specified by the `run` field. Only input parameters
     declared by the target process will be passed through at runtime to the process
-    though additonal parameters may be specified (for use within `valueFrom`
+    though additional parameters may be specified (for use within `valueFrom`
     expressions for instance) - unconnected or unused parameters do not represent an
     error condition.
 
@@ -361,7 +361,7 @@ $graph:
 
     # Picking non-null values among inbound data links
 
-    If present, `pickValue` specifies how to picking non-null values among inbound data links.
+    If present, `pickValue` specifies how to pick non-null values among inbound data links.
 
     `pickValue` is evaluated
       1. Once all source values from upstream step or parameters are available.
@@ -373,7 +373,7 @@ $graph:
     steps may be connected to a single input (`source` is a list), and
     skipped steps produce null values.
 
-    Static type checkers should check for type consistency after infering what the type
+    Static type checkers should check for type consistency after inferring what the type
     will be after `pickValue` is applied, just as they do currently for `linkMerge`.
 
     * **first_non_null**
@@ -556,7 +556,7 @@ $graph:
     Conditionals in CWL are an optional feature and are not required
     to be implemented by all consumers of CWL documents.  An
     implementation that does not support conditionals must return a
-    fatal error when attempting execute a workflow that uses
+    fatal error when attempting to execute a workflow that uses
     conditional constructs the implementation does not support.
 
     # Subworkflows
@@ -726,7 +726,7 @@ $graph:
     - name: steps
       doc: |
         The individual steps that make up the workflow.  Each step is executed when all of its
-        input data links are fufilled.  An implementation may choose to execute
+        input data links are fulfilled.  An implementation may choose to execute
         the steps in a different order than listed and/or execute steps
         concurrently, provided that dependencies between steps are met.
       type:

concepts.md

@@ -347,7 +347,7 @@ subworkflow steps, and so on.  Embedded process objects may optionally
 include `id` fields.
 
 A "$graph" document does not have a process object at the root.
-Instead there is a [`$graph`](SchemaSalad.html#Document_graph) field
+Instead, there is a [`$graph`](SchemaSalad.html#Document_graph) field
 which consists of a list of process objects.  Each process object must
 have an `id` field.  Workflow `run` fields cross-reference other
 processes in the document `$graph` using the `id` of the process

invocation.md

@@ -70,7 +70,7 @@ For compatibility, files may be written to the **system temporary directory**
 which must be located at `/tmp`.  Because the system temporary directory may be
 shared with other processes on the system, files placed in the system temporary
 directory are not guaranteed to be deleted automatically.  A tool
-must not use the system temporary directory as a backchannel communication with
+must not use the system temporary directory as a back-channel communication with
 other tools.  It is valid for the system temporary directory to be the same as
 the designated temporary directory.
 
@@ -98,7 +98,7 @@ systems.
 An implementation may forbid the tool from directly accessing network
 resources.  Correct tools must not assume any network access unless they have
 the 'networkAccess' field of a ['NetworkAccess'](#NetworkAccess) requirement set
-to `true` but even then this does not imply a publically routable IP address or
+to `true` but even then this does not imply a publicly routable IP address or
 the ability to accept inbound connections.
 
 The `runtime` section available in [parameter references](#Parameter_references)