Applied codespell

schema_salad/dotnet/gitignore

@@ -313,8 +313,8 @@ node_modules/
 **/*.Server/ModelManifest.xml
 _Pvt_Extensions
 
-# Paket dependency manager
-.paket/paket.exe
+# Packet dependency manager
+.packet/packet.exe
 paket-files/
 
 # FAKE - F# Make

schema_salad/tests/test_makedoc.py

@@ -177,7 +177,7 @@ def test_multiline_list_entries_word_spacing(metaschema_doc: str) -> None:
     """Hanging indents in Markdown lists don't lead to wordsmushing."""
     assert "as itis poorly documented" not in metaschema_doc
     assert "base URI for the document used toresolve relative" not in metaschema_doc
-    assert "The keys ofthe object are namespace prefixes" not in metaschema_doc
+    assert "The keys of the object are namespace prefixes" not in metaschema_doc
     assert "This field may list URIreferences to documents in RDF-XML" not in metaschema_doc
     assert "defines valid fields thatmake up a record type" not in metaschema_doc
     assert "set of symbols that arevalid value" not in metaschema_doc

schema_salad/tests/test_real_cwl/ICGC-TCGA-PanCancer/complete/vcf_merge.cwl

@@ -6,7 +6,7 @@ label: "merge_vcfs"
 
 doc: |
     This tool will merge VCFs by type (SV, SNV, INDEL). This CWL wrapper was written by Solomon Shorser.
-    The Perl script was originaly written by Brian O'Connor and maintained by Solomon Shorser.
+    The Perl script was originally written by Brian O'Connor and maintained by Solomon Shorser.
 
 $namespaces:
  s: https://schema.org/

schema_salad/tests/test_real_cwl/h3agatk/GATK-complete-WES-Workflow-h3abionet.cwl

@@ -47,7 +47,7 @@ doc: |
   [Picard tools](https://broadinstitute.github.io/picard/) are used to mark duplicated reads in the aligned and sorted BAM file, making thus the files lighter and less prone to errors in the downstream steps of the pipeline.
 
   ## GATK
-  [Genome Analysis Tool Kit](https://software.broadinstitute.org/gatk) refered to as GATK (DePristo et al., 2011) is used to process the data throught multiple steps as described by the [GATK best-practices](https://software.broadinstitute.org/gatk/best-practices/bp_3step.php?case=GermShortWGS) (i.e. figure bellow).
+  [Genome Analysis Tool Kit](https://software.broadinstitute.org/gatk) referred to as GATK (DePristo et al., 2011) is used to process the data throught multiple steps as described by the [GATK best-practices](https://software.broadinstitute.org/gatk/best-practices/bp_3step.php?case=GermShortWGS) (i.e. figure below).
   ![GATK best-practices pipeline](https://raw.githubusercontent.com/h3abionet/h3agatk/master/workflows/GATK/gatk.png)
   The GATK steps are the following:
   	1. Indel Realignment:

schema_salad/tests/test_schema/Base.yml

@@ -286,10 +286,10 @@ $graph:
         noLinkCheck: 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 compatability must be done by checking that an
+        Reasoning about format compatibility must be done by checking that an
         input file format is the same, `owl:equivalentClass` or
         `rdfs:subClassOf` the format required by the input parameter.
         `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if
@@ -350,7 +350,7 @@ $graph:
     the same Directory.
 
     When executing a CommandLineTool, Directories must be recursively staged
-    first and have local values of `path` assigend.
+    first and have local values of `path` assigned.
 
     Directory objects in CommandLineTool output must provide either a
     `location` URI or a `path` property in the context of the tool execution

schema_salad/tests/test_schema/CommandLineTool.yml

@@ -68,7 +68,7 @@ $graph:
       to the CWL Command Line Tool standard:
 
         * The [Directory](#Directory) type.
-        * Syntax simplifcations: denoted by the `map<>` syntax. Example: inputs
+        * Syntax simplifications: denoted by the `map<>` syntax. Example: inputs
           contains a list of items, each with an id. Now one can specify
           a mapping of that identifier to the corresponding
           `CommandInputParameter`.
@@ -761,7 +761,7 @@ $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
@@ -774,18 +774,18 @@ $graph:
         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 [Environement Modules](http://modules.sourceforge.net/),
+        package, a local installation managed by [Environment Modules](http://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
-        computing cluster using Environement Modules could list the IRI
+        computing cluster using Environment Modules could list the IRI
         `https://hpc.example.edu/modules/bowtie-tbb/1.22` to indicate that
         `module load bowtie-tbb/1.1.2` should be executed to make available
         `bowtie` version 1.1.2 compiled with the TBB library prior to running
@@ -922,7 +922,7 @@ $graph:
     Modify the behavior of CommandLineTool to generate a single string
     containing a shell command line.  Each item in the argument list must be
     joined into a string separated by single spaces and quoted to prevent
-    intepretation by the shell, unless `CommandLineBinding` for that argument
+    interpretation by the shell, unless `CommandLineBinding` for that argument
     contains `shellQuote: false`.  If `shellQuote: false` is specified, the
     argument is joined into the command string without quoting, which allows
     the use of shell metacharacters such as `|` for pipes.

schema_salad/tests/test_schema/Process.yml

@@ -310,7 +310,7 @@ $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.
 
 

schema_salad/tests/test_schema/Workflow.yml

@@ -60,7 +60,7 @@ $graph:
       to the CWL Workflow standard:
 
         * The `inputs` and `outputs` fields have been renamed `in` and `out`.
-        * Syntax simplifcations: denoted by the `map<>` syntax. Example: `in`
+        * Syntax simplifications: denoted by the `map<>` syntax. Example: `in`
           contains a list of items, each with an id. Now one can specify
           a mapping of that identifier to the corresponding
           `InputParameter`.
@@ -304,7 +304,7 @@ $graph:
         this input parameter.
 
         If `valueFrom` is a parameter reference or expression, it must be
-        evaluated to yield the actual value to be assiged to the input field.
+        evaluated to yield the actual value to be assigned to the input field.
 
         The `self` value in the parameter reference or expression must be
         1. `null` if there is no `source` field
@@ -519,7 +519,7 @@ $graph:
     The `source` field expresses the dependency of one parameter on another
     such that when a value is associated with the parameter specified by
     `source`, that value is propagated to the destination parameter.  When all
-    data links inbound to a given step are fufilled, the step is ready to
+    data links inbound to a given step are fulfilled, the step is ready to
     execute.
 
     ## Workflow success and failure
@@ -560,7 +560,7 @@ $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: