ccwl - Concise Common Workflow Language (mirror of https://github.com/arunisaac/ccwl)

Age	Commit message (Collapse)	Author
2021-03-22	Remove input->tree abstraction.	Arun Isaac
	<input> objects need to be expanded into CWL in context sensitive ways. There is no simple generalization. * ccwl/ccwl.scm (input->tree): Delete function. (workflow): Expand input->tree.
2021-03-22	Delete input field of <command> object.	Arun Isaac
	* ccwl/ccwl.scm (<command>): Delete input field. (command): Do not set inputs field.
2021-03-21	Print steps enclosing <command> objects correctly.	Arun Isaac
	* ccwl/ccwl.scm (write-cwl): Invoke command->cwl if step encloses <command> object.
2021-03-21	Use both CWL arguments and inputs arrays.	Arun Isaac
	* ccwl/ccwl.scm (<cli-element>): New type. (command->cwl): Put string and expression arguments into the arguments array. Put <input> arguments into the inputs array.
2021-03-21	Add alist filtering utility function.	Arun Isaac
	* ccwl/ccwl.scm (filter-alist): New function. (input->tree): Use filter-alist.
2021-03-21	Set the default output of a pipeline.	Arun Isaac
	* ccwl/ccwl.scm (pipeline): Set the stdout of the last command to be the default output of the pipeline.
2021-03-21	Pull out cwl-version as a separate variable.	Arun Isaac
	* ccwl/ccwl.scm (%cwl-version): New variable. (workflow, command->cwl): Use %cwl-version.
2021-03-21	Add prefix field to <input> object.	Arun Isaac
	* ccwl/ccwl.scm (<input>): Add prefix field. (input): Initialize prefix field. (input-with-prefix): New public function.
2021-03-21	Remove appender for inputs field of <command>.	Arun Isaac
	* ccwl/ccwl.scm (append-command-inputs): Delete function.
2021-03-17	Set default type of outputs to File.	Arun Isaac
	* ccwl/ccwl.scm (output): Set default type to File.
2021-03-17	Set default type of inputs to File.	Arun Isaac
	* ccwl/ccwl.scm (input): Set default type to File.
2021-03-07	Add write-cwl function to write generated CWL to a file.	Arun Isaac
	* ccwl/ccwl.scm: Import (srfi srfi-26) and (ccwl yaml). (write-cwl): New public function.
2021-03-07	Remove field binding from constructor of the <input> type.	Arun Isaac
	* ccwl/ccwl.scm (<input>): Remove field binding from constructor.
2021-03-07	Escape YAML strings that contain the hyphen character.	Arun Isaac
	* ccwl/yaml.scm (display-atom): Escape string if it contains the hyphen character.
2021-03-06	Auto-connect steps by matching identifiers.	Arun Isaac
	* ccwl/ccwl.scm (auto-connect): New function. (workflow): Auto-connect step inputs and outputs before generating <step> record.
2021-03-06	Implement pipeline support.	Arun Isaac
	* ccwl/ccwl.scm (%stdin, %stdout): New variables. (pipeline): New function.
2021-03-06	Rewrite workflow function to output a <step> record.	Arun Isaac
	All user exposed functions should output a <step> record so that they are composable. * ccwl/ccwl.scm (workflow): Rewrite workflow function to output a <step> record.
2021-03-06	Define input=? predicate.	Arun Isaac
	* ccwl/ccwl.scm (input=?): New function.
2021-03-06	Add source field to <input> type.	Arun Isaac
	* ccwl/ccwl.scm (<input>): Add source field. (input): Initialize source field to #f in constructor.
2021-03-06	Remove clitool functions.	Arun Isaac
	* ccwl/ccwl.scm (clitool, clitool-step): Delete functions.
2021-03-06	Add command->cwl rendering function.	Arun Isaac
	* ccwl/ccwl.scm (output->cwl, command->cwl): New functions.
2021-03-06	Add modifier for run field of <step> object.	Arun Isaac
	* ccwl/ccwl.scm (modify-step-run): New function.
2021-03-06	Add field appenders.	Arun Isaac
	* ccwl/ccwl.scm (field-appender, append-step-in, append-step-out, append-command-inputs, append-command-outputs): New functions.
2021-03-06	Introduce <command> type.	Arun Isaac
	* ccwl/ccwl.scm (<command>): New type. (command): New function.
2021-03-06	Delete command parsing functions.	Arun Isaac
	We will not auto-parse commands and try to associate a binding to inputs. If we specify the command using the arguments field of the CWL specification, we don't need to know the base command or the bindings. * ccwl/ccwl.scm: Do not import (srfi srfi-71). (parse-arguments, break-pair, parse-command): Delete functions.
2021-03-06	Remove <intermediate> type.	Arun Isaac
	We will auto-connect inputs and outputs by matching their unique identifiers. * ccwl/ccwl.scm (<intermediate>): Delete type.
2021-03-06	Re-order fields of <input> type.	Arun Isaac
	* ccwl/ccwl.scm (<input>): Re-order <input> fields to be consistent with its constructor.
2021-03-06	Combine <workflow-output> type into <output> type.	Arun Isaac
	The user should not have to distinguish between regular outputs and workflow outputs. * ccwl/ccwl.scm (<output>): Add source field. (output): Add source field to constructor. (<workflow-output>): Delete type. (workflow-output): Delete function.
2021-03-06	Migrate to SRFI-9 records.	Arun Isaac
	Functional setters from (srfi srfi-9 gnu) are very useful. * ccwl/ccwl.scm (<input>, unspecified-default, <output>, <intermediate>, <workflow-output>, <step>): Redefine using SRFI-9 records.
2021-02-27	Rewrite parse-command using break-pair.	Arun Isaac
	* ccwl/ccwl.scm (parse-command): Rewrite using break-pair.
2021-02-27	Add break-pair utility.	Arun Isaac
	* ccwl/ccwl.scm (break-pair): New function. * tests/ccwl.scm: New file. * tests/ccwl.scm ("break-pair", "break-pair: check last elemet handling"): New test cases.
2021-02-27	Display dictionary entries with empty values on the same line.	Arun Isaac
	* ccwl/yaml.scm (display-dictionary-entry): If value is an empty array or dictionary, display it on the same line. (scm->yaml): Go to next line after printing empty array. * tests/yaml.scm: New file. * tests/yaml.scm ("dictionary entries with empty arrays and dictionaries for values must render on the same line"): New test case.
2021-02-27	Add scm->yaml-string.	Arun Isaac
	* ccwl/yaml.scm (scm->yaml-string): New function.
2021-02-27	Rename project to ccwl.	Arun Isaac
	ccwl stands for Concise Common Workflow Language. * generate-cwl/ccwl.scm: Move to ccwl/ccwl.scm. * generate-cwl/yaml.scm: Move to ccwl/yaml.scm.
2021-02-25	Support embedding clitool into a workflow step.	Arun Isaac
	* generate-cwl/generate-cwl.scm: Export intermediate and clitool-step. (<intermediate>): New type. (clitool-step): New function. (workflow): Pull out inputs and intermediate put into <step> objects by clitool-step.
2021-02-23	Initial commit	Arun Isaac