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results-v1.2.1.txt
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Test [1/378] cl_basic_generation: General test of command line generation
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp6tdfurkl --quiet tests/bwa-mem-tool.cwl tests/bwa-mem-job.json
Test [2/378] nested_prefixes_arrays: Test nested prefixes with arrays
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpczaub214 --quiet tests/binding-test.cwl tests/bwa-mem-job.json
Test [3/378] nested_cl_bindings: Test nested command line bindings
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpm0af535m --quiet tests/tmap-tool.cwl tests/tmap-job.json
Test [4/378] cl_optional_inputs_missing: Test command line with optional input (missing)
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpehq3j3nu --quiet tests/cat1-testcli.cwl tests/cat-job.json
Test [5/378] cl_optional_bindings_provided: Test command line with optional input (provided)
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpkpy_0vbo --quiet tests/cat1-testcli.cwl tests/cat-n-job.json
Test [6/378] initworkdir_expreng_requirements: Test InitialWorkDirRequirement ExpressionEngineRequirement.engineConfig feature
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmptxovkq2m --quiet tests/template-tool.cwl tests/cat-job.json
[1;30mWARNING[0m [33mtests/template-tool.cwl:7:9: JSHINT: exports = module.exports = _;
tests/template-tool.cwl:7:9: JSHINT: ^
tests/template-tool.cwl:7:9: JSHINT: W117: 'exports' is not defined.[0m
[1;30mWARNING[0m [33mtests/template-tool.cwl:7:9: JSHINT: exports._ = _;
tests/template-tool.cwl:7:9: JSHINT: ^
tests/template-tool.cwl:7:9: JSHINT: W117: 'exports' is not defined.[0m
[1;30mWARNING[0m [33mtests/template-tool.cwl:7:9: JSHINT: if (typeof module !== 'undefined' && module.exports) {
tests/template-tool.cwl:7:9: JSHINT: ^
tests/template-tool.cwl:7:9: JSHINT: W117: 'module' is not defined.[0m
[1;30mWARNING[0m [33mtests/template-tool.cwl:7:9: JSHINT: exports = module.exports = _;
tests/template-tool.cwl:7:9: JSHINT: ^
tests/template-tool.cwl:7:9: JSHINT: W117: 'module' is not defined.[0m
[1;30mWARNING[0m [33mtests/template-tool.cwl:7:9: JSHINT: return setTimeout(function(){
tests/template-tool.cwl:7:9: JSHINT: ^
tests/template-tool.cwl:7:9: JSHINT: W117: 'setTimeout' is not defined.[0m
[1;30mWARNING[0m [33mtests/template-tool.cwl:7:9: JSHINT: timeout = setTimeout(later, remaining);
tests/template-tool.cwl:7:9: JSHINT: ^
tests/template-tool.cwl:7:9: JSHINT: W117: 'setTimeout' is not defined.[0m
[1;30mWARNING[0m [33mtests/template-tool.cwl:7:9: JSHINT: timeout = setTimeout(later, wait - last);
tests/template-tool.cwl:7:9: JSHINT: ^
tests/template-tool.cwl:7:9: JSHINT: W117: 'setTimeout' is not defined.[0m
[1;30mWARNING[0m [33mtests/template-tool.cwl:7:9: JSHINT: if (!timeout) timeout = setTimeout(later, wait);
tests/template-tool.cwl:7:9: JSHINT: ^
tests/template-tool.cwl:7:9: JSHINT: W117: 'setTimeout' is not defined.[0m
[1;30mWARNING[0m [33mtests/template-tool.cwl:7:9: JSHINT: clearTimeout(timeout);
tests/template-tool.cwl:7:9: JSHINT: ^
tests/template-tool.cwl:7:9: JSHINT: W117: 'clearTimeout' is not defined.[0m
[1;30mWARNING[0m [33mtests/template-tool.cwl:7:9: JSHINT: root._ = previousUnderscore;
tests/template-tool.cwl:7:9: JSHINT: ^
tests/template-tool.cwl:7:9: JSHINT: W117: 'previousUnderscore' is not defined.[0m
[1;30mWARNING[0m [33mtests/template-tool.cwl:7:9: JSHINT: if (typeof define === 'function' && define.amd) {
tests/template-tool.cwl:7:9: JSHINT: ^
tests/template-tool.cwl:7:9: JSHINT: W117: 'define' is not defined.[0m
[1;30mWARNING[0m [33mtests/template-tool.cwl:7:9: JSHINT: define('underscore', [], function() {
tests/template-tool.cwl:7:9: JSHINT: ^
tests/template-tool.cwl:7:9: JSHINT: W117: 'define' is not defined.[0m
[1;30mWARNING[0m [33mtests/template-tool.cwl:8:9: JSHINT: var t = function(s) { return _.template(s, {variable: 'data'})({'inputs': inputs}); };
tests/template-tool.cwl:8:9: JSHINT: ^
tests/template-tool.cwl:8:9: JSHINT: W117: '_' is not defined.[0m
Test [7/378] stdout_redirect_docker: Test command execution in Docker with stdout redirection
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp7ydaloqh --quiet tests/cat3-tool.cwl tests/cat-job.json
Test [8/378] stdout_redirect_shortcut_docker: Test command execution in Docker with shortcut stdout redirection
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpcleedu0i --quiet tests/cat3-tool-shortcut.cwl tests/cat-job.json
Test [9/378] stdout_redirect_mediumcut_docker: Test command execution in Docker with mediumcut stdout redirection
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmphls8tufs --quiet tests/cat3-tool-mediumcut.cwl tests/cat-job.json
Test [10/378] stderr_redirect: Test command line with stderr redirection
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpjcpxz965 --quiet tests/stderr.cwl tests/empty.json
Test [11/378] stderr_redirect_shortcut: Test command line with stderr redirection, brief syntax
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpkicvvo73 --quiet tests/stderr-shortcut.cwl tests/empty.json
Test [12/378] stderr_redirect_mediumcut: Test command line with stderr redirection, named brief syntax
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp57ot4vfd --quiet tests/stderr-mediumcut.cwl tests/empty.json
Test [13/378] stdinout_redirect_docker: Test command execution in Docker with stdin and stdout redirection
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp0yi1z_ci --quiet tests/cat4-tool.cwl tests/cat-job.json
Test [14/378] expression_any: Test default usage of Any in expressions.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpja0rt12j --quiet tests/null-expression1-tool.cwl tests/empty.json
Test [15/378] expression_any_null: Test explicitly passing null to Any type inputs with default values.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpyok6imt4 --quiet tests/null-expression1-tool.cwl tests/null-expression1-job.json
Test [16/378] expression_any_string: Testing the string 'null' does not trip up an Any with a default value.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpdwh72872 --quiet tests/null-expression1-tool.cwl tests/null-expression2-job.json
Test [17/378] expression_any_nodefaultany: Test Any without defaults cannot be unspecified.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpv2bv98bl --quiet tests/null-expression2-tool.cwl tests/empty.json
[1;30mERROR[0m [31mWorkflow error, try again with --debug for more information:
Invalid job input record:
tests/null-expression2-tool.cwl:9:3: Missing required input parameter 'i1'[0m
Test [18/378] expression_any_null_nodefaultany: Test explicitly passing null to Any type without a default value.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp9zuce11o --quiet tests/null-expression2-tool.cwl tests/null-expression1-job.json
[1;30mERROR[0m [31mWorkflow error, try again with --debug for more information:
Invalid job input record:
tests/null-expression2-tool.cwl:9:3: Missing required input parameter 'i1'[0m
Test [19/378] expression_any_nullstring_nodefaultany: Testing the string 'null' does not trip up an Any without a default value.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpxpb06mig --quiet tests/null-expression2-tool.cwl tests/null-expression2-job.json
Test [20/378] any_outputSource_compatibility: Testing Any type compatibility in outputSource
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp4f56ytdh --quiet tests/any-type-compat.cwl tests/any-type-job.json
Test [21/378] stdinout_redirect: Test command execution in with stdin and stdout redirection
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpiwna_iac --quiet tests/cat-tool.cwl tests/cat-job.json
Test [22/378] expression_parseint: Test ExpressionTool with Javascript engine
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpdejfsi78 --quiet tests/parseInt-tool.cwl tests/parseInt-job.json
Test [23/378] expression_outputEval: Test outputEval to transform output
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpajogunao --quiet tests/wc2-tool.cwl tests/wc-job.json
Test [24/378] wf_wc_parseInt: Test two step workflow with imported tools
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwk95jtwj --quiet tests/count-lines1-wf.cwl tests/wc-job.json
Test [25/378] wf_wc_expressiontool: Test two step workflow with inline tools
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpz5rfffk6 --quiet tests/count-lines2-wf.cwl tests/wc-job.json
Test [26/378] wf_wc_scatter: Test single step workflow with Scatter step
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp307a96g2 --quiet tests/count-lines3-wf.cwl tests/count-lines3-job.json
Test [27/378] wf_wc_scatter_multiple_merge: Test single step workflow with Scatter step and two data links connected to same input, default merge behavior
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp4ti5v4cl --quiet tests/count-lines4-wf.cwl tests/count-lines4-job.json
Test [28/378] wf_wc_scatter_multiple_nested: Test single step workflow with Scatter step and two data links connected to same input, nested merge behavior
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpcgp8z5hq --quiet tests/count-lines6-wf.cwl tests/count-lines6-job.json
Test [29/378] wf_wc_scatter_multiple_flattened: Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpnn1s_jru --quiet tests/count-lines7-wf.cwl tests/count-lines6-job.json
Test [30/378] wf_wc_nomultiple: Test when step source is a single-item list and there is no linkMerge, then it not wrapped in a list, and that MultipleInputFeatureRequirement is not required.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpxz2obeju --quiet tests/count-lines13-wf.cwl tests/count-lines4-job.json
Test [31/378] wf_wc_nomultiple_merge_nested: Test when step source is a single-item list and linkMerge is listed, then it is wrapped in a list.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp1pbu_jcr --quiet tests/count-lines19-wf.cwl tests/count-lines4-job.json
Test [32/378] wf_input_default_missing: Test workflow with default value for input parameter (missing)
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpeer5o_7o --quiet tests/count-lines5-wf.cwl tests/empty.json
Test [33/378] wf_input_default_provided: Test workflow with default value for input parameter (provided)
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwszwvxbp --quiet tests/count-lines5-wf.cwl tests/wc-job.json
Test [34/378] wf_default_tool_default: Test that workflow defaults override tool defaults
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmprd9gphi6 --quiet tests/echo-wf-default.cwl tests/empty.json
Test [35/378] envvar_req: Test EnvVarRequirement
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpe63itluc --quiet tests/env-tool1.cwl tests/env-job.json
Test [36/378] wf_scatter_single_param: Test workflow scatter with single scatter parameter
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp9tq2xz9b --quiet tests/scatter-wf1.cwl tests/scatter-job1.json
Test [37/378] wf_scatter_two_nested_crossproduct: Test workflow scatter with two scatter parameters and nested_crossproduct join method
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpgs60w1to --quiet tests/scatter-wf2.cwl tests/scatter-job2.json
Test [38/378] wf_scatter_two_flat_crossproduct: Test workflow scatter with two scatter parameters and flat_crossproduct join method
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpho4yg9o9 --quiet tests/scatter-wf3.cwl#main tests/scatter-job2.json
Test [39/378] wf_scatter_two_dotproduct: Test workflow scatter with two scatter parameters and dotproduct join method
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpd9na831x --quiet tests/scatter-wf4.cwl#main tests/scatter-job2.json
Test [40/378] wf_scatter_emptylist: Test workflow scatter with single empty list parameter
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp4b9bpw7r --quiet tests/scatter-wf1.cwl tests/scatter-empty-job1.json
[1;30mWARNING[0m [33m[job step step1] Notice: scattering over empty input in 'echo_in'. All outputs will be empty.[0m
Test [41/378] wf_scatter_nested_crossproduct_secondempty: Test workflow scatter with two scatter parameters and nested_crossproduct join method with second list empty
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp6eune4kj --quiet tests/scatter-wf2.cwl tests/scatter-empty-job2.json
[1;30mWARNING[0m [33m[job step step1] Notice: scattering over empty input in 'echo_in2'. All outputs will be empty.[0m
Test [42/378] wf_scatter_nested_crossproduct_firstempty: Test workflow scatter with two scatter parameters and nested_crossproduct join method with first list empty
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpewsq7qi0 --quiet tests/scatter-wf3.cwl#main tests/scatter-empty-job3.json
[1;30mWARNING[0m [33m[job step step1] Notice: scattering over empty input in 'echo_in1'. All outputs will be empty.[0m
Test [43/378] wf_scatter_flat_crossproduct_oneempty: Test workflow scatter with two scatter parameters, one of which is empty and flat_crossproduct join method
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp40svpdm3 --quiet tests/scatter-wf3.cwl#main tests/scatter-empty-job2.json
[1;30mWARNING[0m [33m[job step step1] Notice: scattering over empty input in 'echo_in2'. All outputs will be empty.[0m
Test [44/378] wf_scatter_dotproduct_twoempty: Test workflow scatter with two empty scatter parameters and dotproduct join method
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpguzn6x9t --quiet tests/scatter-wf4.cwl#main tests/scatter-empty-job4.json
[1;30mWARNING[0m [33m[job step step1] Notice: scattering over empty input in 'echo_in1', 'echo_in2'. All outputs will be empty.[0m
Test [45/378] any_input_param: Test Any type input parameter
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp83ksegvw --quiet tests/echo-tool.cwl tests/env-job.json
Test [46/378] nested_workflow: Test nested workflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp13vca00n --quiet tests/count-lines8-wf.cwl tests/wc-job.json
Test [47/378] requirement_priority: Test requirement priority
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpdjojabd9 --quiet tests/env-wf1.cwl tests/env-job.json
Test [48/378] requirement_override_hints: Test requirements override hints
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpiynewr1u --quiet tests/env-wf2.cwl tests/env-job.json
Test [49/378] requirement_workflow_steps: Test requirements on workflow steps
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpkunj3kgs --quiet tests/env-wf3.cwl tests/env-job.json
Test [50/378] step_input_default_value: Test default value on step input parameter
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpkdq4c474 --quiet tests/count-lines9-wf.cwl tests/empty.json
Test [51/378] step_input_default_value_nosource: Test use default value on step input parameter with empty source
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwycp47oh --quiet tests/count-lines11-wf.cwl tests/empty.json
[1;30mWARNING[0m [33mWorkflow checker warning:
tests/count-lines11-wf.cwl:6:3: Source 'file1' of type ["null", "File"] may be incompatible
tests/count-lines11-wf.cwl:17:7: with sink 'file1' of type "File"[0m
Test [52/378] step_input_default_value_nullsource: Test use default value on step input parameter with null source
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp9fd3hsi2 --quiet tests/count-lines11-wf.cwl tests/file1-null.json
[1;30mWARNING[0m [33mWorkflow checker warning:
tests/count-lines11-wf.cwl:6:3: Source 'file1' of type ["null", "File"] may be incompatible
tests/count-lines11-wf.cwl:17:7: with sink 'file1' of type "File"[0m
Test [53/378] step_input_default_value_overriden: Test default value on step input parameter overridden by provided source
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpcdaszl9s --quiet tests/count-lines11-wf.cwl tests/cat-job.json
[1;30mWARNING[0m [33mWorkflow checker warning:
tests/count-lines11-wf.cwl:6:3: Source 'file1' of type ["null", "File"] may be incompatible
tests/count-lines11-wf.cwl:17:7: with sink 'file1' of type "File"[0m
Test [54/378] wf_simple: Test simple workflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp1vyhdly4 --quiet tests/revsort.cwl tests/revsort-job.json
Test [55/378] hints_unknown_ignored: Test unknown hints are ignored.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpd443v8xy --quiet tests/cat5-tool.cwl tests/cat-job.json
tests/cat5-tool.cwl:10:3: Warning: checking item
Warning: Field 'class' contains undefined reference to
'http://example.com/BlibberBlubberFakeRequirement'
[1;30mWARNING[0m [33mtests/cat5-tool.cwl:10:3: Warning: checking item
Warning: Field 'class' contains undefined reference to
'http://example.com/BlibberBlubberFakeRequirement'[0m
Test [56/378] initial_workdir_secondary_files_expr: Test InitialWorkDirRequirement linking input files and capturing secondaryFiles on input and output. Also tests the use of a variety of parameter references and expressions in the secondaryFiles field.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmptc1kl_ym --quiet tests/search.cwl#main tests/search-job.json
[1;30mWARNING[0m [33mWorkflow checker warning:
tests/search.cwl:103:13: Source 'result' of type "File" may be incompatible
tests/search.cwl:108:9: with sink 'file' of type "File"[0m
Test [57/378] rename: Test InitialWorkDirRequirement with expression in filename.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmprmr9yf7g --quiet tests/rename.cwl tests/rename-job.json
Test [58/378] initial_workdir_trailingnl: Test if trailing newline is present in file entry in InitialWorkDir
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpblxujnyk --quiet tests/iwdr-entry.cwl tests/string-job.json
Test [59/378] inline_expressions: Test inline expressions
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpf1iovt7g --quiet tests/wc4-tool.cwl tests/wc-job.json
Test [60/378] schemadef_req_tool_param: Test SchemaDefRequirement definition used in tool parameter
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpectpmprt --quiet tests/schemadef-tool.cwl tests/schemadef-job.json
Test [61/378] schemadef_req_wf_param: Test SchemaDefRequirement definition used in workflow parameter
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp10cmoiv9 --quiet tests/schemadef-wf.cwl tests/schemadef-job.json
Test [62/378] param_evaluation_noexpr: Test parameter evaluation, no support for JS expressions
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp162hqwlt --quiet tests/params.cwl tests/empty.json
Test [63/378] param_evaluation_expr: Test parameter evaluation, with support for JS expressions
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpg5s8wn7t --quiet tests/params2.cwl tests/empty.json
Test [64/378] metadata: Test metadata
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpjrzqha8x --quiet tests/metadata.cwl tests/cat-job.json
Test [65/378] format_checking: Test simple format checking.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpbwbiznsk --quiet tests/formattest.cwl tests/formattest-job.json
Test [66/378] format_checking_subclass: Test format checking against ontology using subclassOf.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpraglz80x --quiet tests/formattest2.cwl tests/formattest2-job.json
Test [67/378] format_checking_equivalentclass: Test format checking against ontology using equivalentClass.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpbk73q8hc --quiet tests/formattest3.cwl tests/formattest2-job.json
Test [68/378] output_secondaryfile_optional: Test optional output file and optional secondaryFile on output.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpmtvcie5d --quiet tests/optional-output.cwl tests/cat-job.json
Test [69/378] valuefrom_ignored_null: Test that valueFrom is ignored when the parameter is null
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp_11m31pq --quiet tests/vf-concat.cwl tests/empty.json
Test [70/378] valuefrom_secondexpr_ignored: Test that second expression in concatenated valueFrom is not ignored
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwxywzjq8 --quiet tests/vf-concat.cwl tests/cat-job.json
Test [71/378] valuefrom_wf_step: Test valueFrom on workflow step.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp34v9_m1p --quiet tests/step-valuefrom-wf.cwl tests/step-valuefrom-wf.json
Test [72/378] valuefrom_wf_step_multiple: Test valueFrom on workflow step with multiple sources
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpppp1kqx7 --quiet tests/step-valuefrom2-wf.cwl tests/step-valuefrom-job.json
Test [73/378] valuefrom_wf_step_other: Test valueFrom on workflow step referencing other inputs
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmprh1yq59q --quiet tests/step-valuefrom3-wf.cwl tests/step-valuefrom-job.json
Test [74/378] record_output_binding: Test record type output binding.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpbdg5r6du --quiet tests/record-output.cwl tests/record-output-job.json
Test [75/378] docker_json_output_path: Test support for reading cwl.output.json when running in a Docker container and just 'path' is provided.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmprchvj_wu --quiet tests/test-cwl-out.cwl tests/empty.json
Test [76/378] docker_json_output_location: Test support for reading cwl.output.json when running in a Docker container and just 'location' is provided.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpi5k3mkwo --quiet tests/test-cwl-out2.cwl tests/empty.json
Test [77/378] json_output_path_relative: Test support for reading cwl.output.json where 'path' is relative path in output dir.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpozqiei5h --quiet tests/test-cwl-out3.cwl tests/empty.json
Test [78/378] json_output_location_relative: Test support for reading cwl.output.json where 'location' is relative reference to output dir.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpmky97o04 --quiet tests/test-cwl-out4.cwl tests/empty.json
Test [79/378] multiple_glob_expr_list: Test support for returning multiple glob patterns from expression
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmplkkve8ic --quiet tests/glob-expr-list.cwl tests/abc.json
Test [80/378] wf_scatter_oneparam_valuefrom: Test workflow scatter with single scatter parameter and two valueFrom on step input (first and current el)
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwg5x9x08 --quiet tests/scatter-valuefrom-wf1.cwl tests/scatter-valuefrom-job1.json
Test [81/378] wf_scatter_twoparam_nested_crossproduct_valuefrom: Test workflow scatter with two scatter parameters and nested_crossproduct join method and valueFrom on step input
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpxz37jvw3 --quiet tests/scatter-valuefrom-wf2.cwl tests/scatter-valuefrom-job2.json
Test [82/378] wf_scatter_twoparam_flat_crossproduct_valuefrom: Test workflow scatter with two scatter parameters and flat_crossproduct join method and valueFrom on step input
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpfylt14_y --quiet tests/scatter-valuefrom-wf3.cwl#main tests/scatter-valuefrom-job2.json
Test [83/378] wf_scatter_twoparam_dotproduct_valuefrom: Test workflow scatter with two scatter parameters and dotproduct join method and valueFrom on step input
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp164fictz --quiet tests/scatter-valuefrom-wf4.cwl#main tests/scatter-valuefrom-job2.json
Test [84/378] wf_scatter_oneparam_valuefrom_twice_current_el: Test workflow scatter with single scatter parameter and two valueFrom on step input (current el twice)
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpw977deh9 --quiet tests/scatter-valuefrom-wf5.cwl tests/scatter-valuefrom-job1.json
Test [85/378] wf_scatter_oneparam_valueFrom: Test valueFrom eval on scattered input parameter
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmprwrh5xkj --quiet tests/scatter-valuefrom-wf6.cwl tests/scatter-valuefrom-job3.json
Test [86/378] wf_two_inputfiles_namecollision: Test workflow two input files with same name.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpyib7a_rx --quiet tests/conflict-wf.cwl#collision tests/conflict-job.json
Test [87/378] directory_input_param_ref: Test directory input with parameter reference
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmprrj3oowl --quiet tests/dir.cwl tests/dir-job.yml
Test [88/378] directory_input_docker: Test directory input in Docker
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwqldw6b8 --quiet tests/dir2.cwl tests/dir-job.yml
Test [89/378] directory_output: Test directory output
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp28zdbwqz --quiet tests/dir3.cwl tests/dir3-job.yml
Test [90/378] directory_secondaryfiles: Test directories in secondaryFiles
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpaoybr1rk --quiet tests/dir4.cwl tests/dir4-job.yml
Test [91/378] dynamic_initial_workdir: Test dynamic initial work dir
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp4kk19znl --quiet tests/dir5.cwl tests/dir-job.yml
Test [92/378] writable_stagedfiles: Test writable staged files.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpxwjvt8mt --quiet tests/stagefile.cwl tests/stagefile-job.yml
Test [93/378] input_file_literal: Test file literal as input
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpgg2mdglq --quiet tests/cat3-tool.cwl tests/file-literal.yml
Test [94/378] initial_workdir_expr: Test expression in InitialWorkDir listing
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpbtlwfe2i --quiet tests/linkfile.cwl tests/arguments-job.yml
Test [95/378] nameroot_nameext_stdout_expr: Test nameroot/nameext expression in arguments, stdout
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpfgs40mbh --quiet tests/nameroot.cwl tests/wc-job.json
Test [96/378] input_dir_inputbinding: Test directory input with inputBinding
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpmkgbw7f5 --quiet tests/dir6.cwl tests/dir-job.yml
Test [97/378] cl_gen_arrayofarrays: Test command line generation of array-of-arrays
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpf0dvbixt --quiet tests/nested-array.cwl tests/nested-array-job.yml
Test [98/378] env_home_tmpdir: Test $HOME and $TMPDIR are set correctly
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp07hy8isr --quiet tests/envvar.cwl tests/empty.json
Test [99/378] env_home_tmpdir_docker: Test $HOME and $TMPDIR are set correctly in Docker
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp4mvjq655 --quiet tests/envvar2.cwl tests/empty.json
Test [100/378] expressionlib_tool_wf_override: Test that expressionLib requirement of individual tool step overrides expressionLib of workflow.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp32m2_kcc --quiet tests/js-expr-req-wf.cwl#wf tests/empty.json
Test [101/378] initial_workdir_output: Test output of InitialWorkDir
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpu25q2u4f --quiet tests/initialworkdirrequirement-docker-out.cwl tests/initialworkdirrequirement-docker-out-job.json
Test [102/378] embedded_subworkflow: Test embedded subworkflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpgff8odwa --quiet tests/count-lines10-wf.cwl tests/wc-job.json
Test [103/378] filesarray_secondaryfiles: Test required, optional and null secondaryFiles on array of files.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwxxm_yil --quiet tests/docker-array-secondaryfiles.cwl tests/docker-array-secondaryfiles-job.json
Test [104/378] filesarray_secondaryfiles2: Test required, optional and null secondaryFiles on array of files.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp63kpq2kh --quiet tests/docker-array-secondaryfiles.cwl tests/docker-array-secondaryfiles-job2.json
[1;30mERROR[0m [31mWorkflow error, try again with --debug for more information:
Missing required secondary file '.dat' from file object: {
"class": "File",
"location": "file:///conformance/cwl-v1.2-1.2.1_proposed/tests/ref.fasta",
"size": 12010,
"basename": "ref.fasta",
"nameroot": "ref",
"nameext": ".fasta",
"secondaryFiles": [
{
"location": "file:///conformance/cwl-v1.2-1.2.1_proposed/tests/ref.fasta.fai",
"basename": "ref.fasta.fai",
"class": "File"
}
]
}[0m
Test [105/378] exprtool_directory_literal: Test directory literal output created by ExpressionTool
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp97a_ssyf --quiet tests/dir7.cwl tests/dir7.yml
Test [106/378] exprtool_file_literal: Test file literal output created by ExpressionTool
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpbk_pha40 --quiet tests/file-literal-ex.cwl tests/empty.json
Test [107/378] dockeroutputdir: Test dockerOutputDirectory
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpn3sl__nj --quiet tests/docker-output-dir.cwl tests/empty.json
[1;30mERROR[0m [31mFound a queued exception, canceling outstanding futures[0m
[1;30mERROR[0m [31mWaiting for canceled futures to finish[0m
[1;30mERROR[0m [31mWorkflow or tool uses unsupported feature:
Error: feature DockerRequirement.dockerOutputDirectory is not supported[0m
Test [108/378] hints_import: Test hints with $import
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp4y8woat3 --quiet tests/imported-hint.cwl tests/empty.json
Test [109/378] default_path_notfound_warning: Test warning instead of error when default path is not found
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp2yxtagn8 --quiet tests/default_path.cwl tests/default_path_job.yml
Test [110/378] inlinejs_req_expressions: Test InlineJavascriptRequirement with multiple expressions in the same tool
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp4yf89eth --quiet tests/inline-js.cwl tests/empty.json
Test [111/378] input_dir_recurs_copy_writable: Test if a writable input directory is recursively copied and writable
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp7u83u57g --quiet tests/recursive-input-directory.cwl tests/recursive-input-directory.yml
Test [112/378] null_missing_params: Test that missing parameters are null (not undefined) in expression
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmprmv4mb_8 --quiet tests/null-defined.cwl tests/empty.json
Test [113/378] param_notnull_expr: Test that provided parameter is not null in expression
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmptla0p1u6 --quiet tests/null-defined.cwl tests/cat-job.json
Test [114/378] wf_compound_doc: Test compound workflow document
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpsi20e5fk --quiet tests/revsort-packed.cwl#main tests/revsort-job.json
Test [115/378] nameroot_nameext_generated: Test that nameroot and nameext are generated from basename at execution time by the runner
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp18w7pz5w --quiet tests/basename-fields-test.cwl tests/basename-fields-job.yml
Test [116/378] initialworkpath_output: Test that file path in $(inputs) for initialworkdir is in $(outdir).
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmphw6izjui --quiet tests/initialwork-path.cwl tests/wc-job.json
Test [117/378] wf_scatter_twopar_oneinput_flattenedmerge: Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior. Workflow inputs are set as list
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp4npvo83j --quiet tests/count-lines12-wf.cwl tests/count-lines6-job.json
Test [118/378] wf_multiplesources_multipletypes: Test step input with multiple sources with multiple types
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpvprixf_k --quiet tests/sum-wf.cwl tests/sum-job.json
Test [119/378] shelldir_notinterpreted: Test that shell directives are not interpreted.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpehcy7tco --quiet tests/shellchar.cwl tests/empty.json
Test [120/378] shelldir_quoted: Test that shell directives are quoted.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmphmxcnvpj --quiet tests/shellchar2.cwl tests/empty.json
Test [121/378] initial_workdir_empty_writable: Test empty writable dir with InitialWorkDirRequirement
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmprdm2ar4j --quiet tests/writable-dir.cwl tests/empty.json
Test [122/378] initial_workdir_empty_writable_docker: Test empty writable dir with InitialWorkDirRequirement inside Docker
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpfh4ttypw --quiet tests/writable-dir-docker.cwl tests/empty.json
Test [123/378] dynamic_resreq_inputs: Test dynamic resource reqs referencing inputs
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpedv3eg8m --quiet tests/dynresreq.cwl tests/dynresreq-job.yaml
Test [124/378] fileliteral_input_docker: Test file literal as input without Docker
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpirlbtn7n --quiet tests/cat3-nodocker.cwl tests/file-literal.yml
Test [125/378] outputbinding_glob_sorted: Test that OutputBinding.glob is sorted as specified by POSIX
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpivdi2vpf --quiet tests/glob_test.cwl tests/empty.json
Test [126/378] initialworkdir_nesteddir: Test InitialWorkDirRequirement with a nested directory structure from another step
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpipsmgj0u --quiet tests/iwdr_with_nested_dirs.cwl tests/empty.json
Test [127/378] booleanflags_cl_noinputbinding: Test that boolean flags do not appear on command line if inputBinding is empty and not null
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpsqgdb17k --quiet tests/bool-empty-inputbinding.cwl tests/bool-empty-inputbinding-job.json
Test [128/378] expr_reference_self_noinput: Test that expression engine does not fail to evaluate reference to self with unprovided input
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpdr3gpajm --quiet tests/stage-unprovided-file.cwl tests/empty.json
Test [129/378] success_codes: Test successCodes
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp3pptdllk --quiet tests/exit-success.cwl tests/empty.json
Test [130/378] dynamic_resreq_wf: Test simple workflow with a dynamic resource requirement
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp34lj4nby --quiet tests/dynresreq-workflow.cwl tests/dynresreq-job.yaml
Test [131/378] cl_empty_array_input: Test that empty array input does not add anything to command line
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpa_aoi6nv --quiet tests/empty-array-input.cwl tests/empty-array-job.json
Test [132/378] resreq_step_overrides_wf: Test that ResourceRequirement on a step level redefines requirement on the workflow level
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpp6iny2ga --quiet tests/steplevel-resreq.cwl tests/empty.json
Test [133/378] valuefrom_constant_overrides_inputs: Test valueFrom with constant value overriding provided array inputs
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp7coge9h8 --quiet tests/valueFrom-constant.cwl tests/array-of-strings-job.yml
Test [134/378] dynamic_resreq_filesizes: Test dynamic resource reqs referencing the size of Files inside a Directory
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp2nyqzj68 --quiet tests/dynresreq-dir.cwl tests/dynresreq-dir-job.yaml
Test [135/378] wf_step_connect_undeclared_param: Test that it is not an error to connect a parameter to a workflow step, even if the parameter doesn't appear in the `run` process inputs.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpe3mv_gcs --quiet tests/pass-unconnected.cwl tests/empty.json
[1;30mWARNING[0m [33mWorkflow checker warning:
tests/pass-unconnected.cwl:18:7: 'in2' is not an input parameter of
file:///conformance/cwl-v1.2-1.2.1_proposed/tests/echo-tool.cwl,
expected in[0m
Test [136/378] wf_step_access_undeclared_param: Test that parameters that don't appear in the `run` process inputs are not present in the input object used to run the tool.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpptwa1hob --quiet tests/fail-unconnected.cwl tests/empty.json
[1;30mWARNING[0m [33mWorkflow checker warning:
tests/fail-unconnected.cwl:18:7: 'in2' is not an input parameter of
file:///conformance/cwl-v1.2-1.2.1_proposed/tests/fail-unspecified-input.cwl,
expected in[0m
Syntax error in parameter reference 'inputs.in2': inputs does not contain key 'in2'.. This could be due to using Javascript code without specifying InlineJavascriptRequirement.
Traceback (most recent call last):
File "/usr/local/lib/python3.10/site-packages/cwl_utils/expression.py", line 315, in do_eval
return interpolate(
File "/usr/local/lib/python3.10/site-packages/cwl_utils/expression.py", line 215, in interpolate
e = evaluator(
File "/usr/local/lib/python3.10/site-packages/cwl_utils/expression.py", line 164, in evaluator
raise JavascriptException(
cwl_utils.errors.JavascriptException: Syntax error in parameter reference 'inputs.in2': inputs does not contain key 'in2'.. This could be due to using Javascript code without specifying InlineJavascriptRequirement.
[1;30mERROR[0m [31mException on step 'step1'[0m
[1;30mERROR[0m [31m[step step1] Cannot make job: tests/fail-unspecified-input.cwl:13:33: Expression evaluation error:
tests/fail-unspecified-input.cwl:13:33: Syntax error in parameter reference 'inputs.in2': inputs does not contain key 'in2'.. This could be due to using Javascript code without specifying InlineJavascriptRequirement.[0m
[1;30mWARNING[0m [33mFinal process status is permanentFail[0m
Test [137/378] env_home_tmpdir_docker_no_return_code: Test $HOME and $TMPDIR are set correctly in Docker without using return code
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpo_3dqreb --quiet tests/envvar3.cwl tests/empty.json
Test [138/378] wf_scatter_oneparam_valuefrom_inputs: Test workflow scatter with single scatter parameter and two valueFrom using $inputs (first and current el)
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpsf848i5z --quiet tests/scatter-valuefrom-inputs-wf1.cwl tests/scatter-valuefrom-job1.json
Test [139/378] packed_import_schema: SchemaDefRequirement with $import, and packed
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpj9cav7wv --quiet tests/import_schema-def_packed.cwl tests/import_schema-def_job.yml
Test [140/378] job_input_secondary_subdirs: Test specifying secondaryFiles in subdirectories of the job input document.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmptww3wxp7 --quiet tests/dir4.cwl tests/dir4-subdir-1-job.yml
Test [141/378] job_input_subdir_primary_and_secondary_subdirs: Test specifying secondaryFiles in same subdirectory of the job input as the primary input file.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpc66jc0ix --quiet tests/dir4.cwl tests/dir4-subdir-2-job.yml
Test [142/378] scatter_embedded_subworkflow: Test simple scatter over an embedded subworkflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpixoxio_o --quiet tests/count-lines18-wf.cwl tests/count-lines3-job.json
Test [143/378] scatter_multi_input_embedded_subworkflow: Test simple multiple input scatter over an embedded subworkflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp3y4am0to --quiet tests/count-lines14-wf.cwl tests/count-lines4-job.json
Test [144/378] workflow_embedded_subworkflow_embedded_subsubworkflow: Test twice nested subworkflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp17vcem7v --quiet tests/count-lines15-wf.cwl tests/wc-job.json
Test [145/378] workflow_embedded_subworkflow_with_tool_and_subsubworkflow: Test subworkflow of mixed depth with tool first
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwnvjskw3 --quiet tests/count-lines16-wf.cwl tests/wc-job.json
Test [146/378] workflow_embedded_subworkflow_with_subsubworkflow_and_tool: Test subworkflow of mixed depth with tool after
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpaycmeuvz --quiet tests/count-lines17-wf.cwl tests/wc-job.json
Test [147/378] workflow_records_inputs_and_outputs: Test record type inputs to and outputs from workflows.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmppqwu8u4p --quiet tests/record-output-wf.cwl tests/record-output-job.json
Test [148/378] workflow_integer_input: Test integer workflow input and outputs
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp1_e7a48m --quiet tests/io-int-wf.cwl tests/io-int.json
Test [149/378] workflow_integer_input_optional_specified: Test optional integer workflow inputs (specified)
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpk4fysqql --quiet tests/io-int-optional-wf.cwl tests/io-int.json
Test [150/378] workflow_integer_input_optional_unspecified: Test optional integer workflow inputs (unspecified)
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp7vexd9ux --quiet tests/io-int-optional-wf.cwl tests/empty.json
Test [151/378] workflow_integer_input_default_specified: Test default integer workflow inputs (specified)
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpxmblhaca --quiet tests/io-int-default-wf.cwl tests/io-int.json
Test [152/378] workflow_integer_input_default_unspecified: Test default integer workflow inputs (unspecified)
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpdu_kx5pl --quiet tests/io-int-default-wf.cwl tests/empty.json
Test [153/378] workflow_integer_input_default_and_tool_integer_input_default: Test default integer tool and workflow inputs (unspecified)
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp_o3a2hyu --quiet tests/io-int-default-tool-and-wf.cwl tests/empty.json
Test [154/378] workflow_file_input_default_unspecified: Test File input with default unspecified to workflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmppd5rd65o --quiet tests/io-file-default-wf.cwl tests/empty.json
Test [155/378] workflow_file_input_default_specified: Test File input with default specified to workflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpy7qecz1m --quiet tests/io-file-default-wf.cwl tests/default_path_job.yml
Test [156/378] clt_optional_union_input_file_or_files_with_array_of_one_file_provided: Test input union type or File or File array to a tool with one file in array specified.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp8iv1kyyu --quiet tests/io-file-or-files.cwl tests/job-input-array-one-empty-file.json
Test [157/378] clt_optional_union_input_file_or_files_with_many_files_provided: Test input union type or File or File array to a tool with a few files in array specified.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpt3kkee_5 --quiet tests/io-file-or-files.cwl tests/job-input-array-few-files.json
Test [158/378] clt_optional_union_input_file_or_files_with_single_file_provided: Test input union type or File or File array to a tool with one file specified.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpccslwuvf --quiet tests/io-file-or-files.cwl tests/job-input-one-file.json
Test [159/378] clt_optional_union_input_file_or_files_with_nothing_provided: Test input union type or File or File array to a tool with null specified.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpkj5rgna4 --quiet tests/io-file-or-files.cwl tests/job-input-null.json
Test [160/378] clt_any_input_with_integer_provided: Test Any parameter with integer input to a tool
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmprpld1d14 --quiet tests/io-any-1.cwl tests/io-any-int.json
Test [161/378] clt_any_input_with_string_provided: Test Any parameter with string input to a tool
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpcxaps62t --quiet tests/io-any-1.cwl tests/io-any-string.json
Test [162/378] clt_any_input_with_file_provided: Test Any parameter with file input to a tool
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp1jik3ekm --quiet tests/io-any-1.cwl tests/io-any-file.json
Test [163/378] clt_any_input_with_mixed_array_provided: Test Any parameter with array input to a tool
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpnc4b2vxf --quiet tests/io-any-1.cwl tests/io-any-array.json
Test [164/378] clt_any_input_with_record_provided: Test Any parameter with record input to a tool
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpe5n40j4c --quiet tests/io-any-1.cwl tests/io-any-record.json
Test [165/378] workflow_any_input_with_integer_provided: Test Any parameter with integer input to a workflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp5tnzd_ux --quiet tests/io-any-wf-1.cwl tests/io-any-int.json
Test [166/378] workflow_any_input_with_string_provided: Test Any parameter with string input to a workflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmppxe_uhds --quiet tests/io-any-wf-1.cwl tests/io-any-string.json
Test [167/378] workflow_any_input_with_file_provided: Test Any parameter with file input to a workflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmptekrwz4g --quiet tests/io-any-wf-1.cwl tests/io-any-file.json
Test [168/378] workflow_any_input_with_mixed_array_provided: Test Any parameter with array input to a workflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp70713wvj --quiet tests/io-any-wf-1.cwl tests/io-any-array.json
Test [169/378] workflow_any_input_with_record_provided: Test Any parameter with record input to a tool
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpc607b1op --quiet tests/io-any-wf-1.cwl tests/io-any-record.json
Test [170/378] workflow_union_default_input_unspecified: Test union type input to workflow with default unspecified
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpynj9v9rm --quiet tests/io-union-input-default-wf.cwl tests/empty.json
Test [171/378] workflow_union_default_input_with_file_provided: Test union type input to workflow with default specified as file
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpudj0b890 --quiet tests/io-union-input-default-wf.cwl tests/io-any-file.json
Test [172/378] workflowstep_valuefrom_string: Test valueFrom on workflow step from literal (string).
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp6ildflk5 --quiet tests/step-valuefrom4-wf.cwl tests/empty.json
Test [173/378] workflowstep_valuefrom_file_basename: Test valueFrom on workflow step using basename.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp1n78pv2h --quiet tests/step-valuefrom5-wf.cwl tests/wc-job.json
Test [174/378] expression_tool_int_array_output: Test output arrays in a tool (with ints).
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpeqe9j2og --quiet tests/output-arrays-int.cwl tests/output-arrays-int-job.json
Test [175/378] workflowstep_int_array_input_output: Test output arrays in a workflow (with ints).
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpkvhnm8z_ --quiet tests/output-arrays-int-wf.cwl tests/output-arrays-int-job.json
Test [176/378] workflow_file_array_output: Test output arrays in a workflow (with Files).
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp4kuitt45 --quiet tests/output-arrays-file-wf.cwl tests/output-arrays-file-job.json
Test [177/378] docker_entrypoint: Test Docker ENTRYPOINT usage
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpmt4f5lju --quiet tests/docker-run-cmd.cwl tests/empty.json
[1;30mERROR[0m [31mFound a queued exception, canceling outstanding futures[0m
[1;30mERROR[0m [31mWaiting for canceled futures to finish[0m
[1;30mERROR[0m [31mWorkflow error, try again with --debug for more information:
("Error collecting output for parameter 'cow': tests/docker-run-cmd.cwl:11:7: Did not find output
file with glob
pattern: ['cow'].",
{})[0m
Test 177 failed: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpmt4f5lju --quiet tests/docker-run-cmd.cwl tests/empty.json
Test Docker ENTRYPOINT usage
Returned non-zero
Test [178/378] clt_file_size_property_with_empty_file: Test use of size in expressions for an empty file
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp32sdr40e --quiet tests/size-expression-tool.cwl tests/job-input-array-one-empty-file.json
Test [179/378] clt_file_size_property_with_multi_file: Test use of size in expressions for a few files
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp127ojtbs --quiet tests/size-expression-tool.cwl tests/job-input-array-few-files.json
Test [180/378] any_without_defaults_unspecified_fails: Test Any without defaults, unspecified, should fail.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp5rv7l9nt --quiet tests/echo-tool.cwl tests/null-expression-echo-job.json
[1;30mERROR[0m [31mWorkflow error, try again with --debug for more information:
Invalid job input record:
tests/echo-tool.cwl:6:3: Missing required input parameter 'in'[0m
Test [181/378] any_without_defaults_specified_fails: Test Any without defaults, specified, should fail.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp2dj4wqbo --quiet tests/echo-tool.cwl tests/null-expression1-job.json
[1;30mERROR[0m [31mWorkflow error, try again with --debug for more information:
Invalid job input record:
tests/echo-tool.cwl:6:3: Missing required input parameter 'in'[0m
Test [182/378] step_input_default_value_noexp: Test default value on step input parameter, no ExpressionTool
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpqtxl9qxz --quiet tests/count-lines9-wf-noET.cwl tests/empty.json
Test [183/378] step_input_default_value_overriden_noexp: Test default value on step input parameter overridden by provided source, no ExpressionTool
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpq94nu7ue --quiet tests/count-lines11-wf-noET.cwl tests/cat-job.json
[1;30mWARNING[0m [33mWorkflow checker warning:
tests/count-lines11-wf-noET.cwl:6:3: Source 'file1' of type ["null", "File"] may be incompatible
tests/count-lines11-wf-noET.cwl:17:7: with sink 'file1' of type "File"[0m
Test [184/378] nested_workflow_noexp: Test nested workflow, without ExpressionTool
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpgrjapva2 --quiet tests/count-lines8-wf-noET.cwl tests/wc-job.json
Test [185/378] wf_multiplesources_multipletypes_noexp: Test step input with multiple sources with multiple types, without ExpressionTool
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpubdk2z3o --quiet tests/sum-wf-noET.cwl tests/sum-job.json
Test [186/378] dynamic_resreq_wf_optional_file_default: Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The CommandLineTool input has a default value (a local file) and the workflow nor the workflow step does not provide any value for this input.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmptmhmz_17 --quiet tests/dynresreq-workflow-tooldefault.cwl tests/empty.json
[1;30mWARNING[0m [33mWorkflow checker warning:
tests/dynresreq-workflow-tooldefault.cwl:6:3: Source 'special_file' of type ["null", "File"] may
be incompatible
tests/dynresreq-workflow-tooldefault.cwl:15:7: with sink 'special_file' of type "File"[0m
Test [187/378] dynamic_resreq_wf_optional_file_step_default: Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow step provides a default value (a local file) for this input and the workflow itself does not provide any value for this input.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpn4v7cvxx --quiet tests/dynresreq-workflow-stepdefault.cwl tests/empty.json
[1;30mWARNING[0m [33mWorkflow checker warning:
tests/dynresreq-workflow-stepdefault.cwl:6:3: Source 'special_file' of type ["null", "File"] may
be incompatible
tests/dynresreq-workflow-stepdefault.cwl:15:7: with sink 'special_file' of type "File"[0m
Test [188/378] dynamic_resreq_wf_optional_file_wf_default: Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow itelf provides a default value (a local file) for this input.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpmdo2pq5k --quiet tests/dynresreq-workflow-inputdefault.cwl tests/empty.json
Test [189/378] step_input_default_value_overriden_2nd_step: Test default value on step input parameter overridden by provided source. With passthrough first step
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmph937perd --quiet tests/count-lines11-extra-step-wf.cwl tests/cat-job.json
[1;30mWARNING[0m [33mWorkflow checker warning:
tests/count-lines11-extra-step-wf.cwl:6:3: Source 'file1' of type ["null", "File"] may be
incompatible
tests/count-lines11-extra-step-wf.cwl:17:7: with sink 'file1' of type "File"[0m
Test [190/378] step_input_default_value_overriden_2nd_step_noexp: Test default value on step input parameter overridden by provided source. With passthrough first step and no ExpressionTool
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpgu6hoh3y --quiet tests/count-lines11-extra-step-wf-noET.cwl tests/cat-job.json
[1;30mWARNING[0m [33mWorkflow checker warning:
tests/count-lines11-extra-step-wf-noET.cwl:6:3: Source 'file1' of type ["null", "File"] may be
incompatible
tests/count-lines11-extra-step-wf-noET.cwl:17:7: with sink 'file1' of type "File"[0m
Test [191/378] step_input_default_value_overriden_2nd_step_null: Test default value on step input parameter overridden by provided source. With null producing first step
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpk7lssf8_ --quiet tests/count-lines11-null-step-wf.cwl tests/empty.json
Test [192/378] step_input_default_value_overriden_2nd_step_null_noexp: Test default value on step input parameter overridden by provided source. With null producing first step and no ExpressionTool
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp8fz_zh7i --quiet tests/count-lines11-null-step-wf-noET.cwl tests/empty.json
Test [193/378] stdin_from_directory_literal_with_local_file: Pipe to stdin from user provided local File via a Directory literal
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpz7lc64x2 --quiet tests/cat-from-dir.cwl tests/cat-from-dir-job.yaml
Test [194/378] stdin_from_directory_literal_with_literal_file: Pipe to stdin from literal File via a Directory literal
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp_xycl540 --quiet tests/cat-from-dir.cwl tests/cat-from-dir-with-literal-file.yaml
Test [195/378] directory_literal_with_literal_file_nostdin: Test non-stdin reference to literal File via a Directory literal
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpmplmk6p7 --quiet tests/cat3-from-dir.cwl tests/cat-from-dir-with-literal-file.yaml
Test [196/378] no_inputs_commandlinetool: Test CommandLineTool without inputs
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmphtdjptps --quiet tests/no-inputs-tool.cwl
Test [197/378] no_outputs_commandlinetool: Test CommandLineTool without outputs
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp1kem10vf --quiet tests/no-outputs-tool.cwl tests/cat-job.json
Test [198/378] no_inputs_workflow: Test Workflow without inputs
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpt63mjs6m --quiet tests/no-inputs-wf.cwl
Test [199/378] no_outputs_workflow: Test Workflow without outputs
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpalfjilo5 --quiet tests/no-outputs-wf.cwl tests/cat-job.json
Test [200/378] anonymous_enum_in_array: Test an anonymous enum inside an array inside a record
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpngyv1icv --quiet tests/anon_enum_inside_array.cwl tests/anon_enum_inside_array.yml
Test [201/378] schema-def_anonymous_enum_in_array: Test an anonymous enum inside an array inside a record, SchemaDefRequirement
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpf3u0asu1 --quiet tests/anon_enum_inside_array_inside_schemadef.cwl tests/anon_enum_inside_array_inside_schemadef.yml
Test [202/378] stdin_shorcut: Test command execution in with stdin and stdout redirection using stdin shortcut
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpua6j2x3x --quiet tests/cat-tool-shortcut.cwl tests/wc-job.json
Test [203/378] secondary_files_in_unnamed_records: Test secondaryFiles on anonymous record fields
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpnbza1z64 --quiet tests/record-in-secondaryFiles.cwl tests/record-secondaryFiles-job.yml
Test [204/378] secondary_files_in_named_records: Test secondaryFiles on SchemaDefRequirement record fields
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpdap0uis_ --quiet tests/record-sd-secondaryFiles.cwl tests/record-secondaryFiles-job.yml
Test [205/378] secondary_files_in_output_records: Test secondaryFiles on output record fields
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp21at5_yi --quiet tests/record-out-secondaryFiles.cwl tests/empty.json
Test [206/378] secondary_files_workflow_propagation: Test secondaryFiles propagation through workflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpkmxetl_q --quiet tests/record-in-secondaryFiles-wf.cwl tests/record-secondaryFiles-job.yml
Test [207/378] secondary_files_missing: Test checking when secondaryFiles are missing
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpr3sdmti9 --quiet tests/record-in-secondaryFiles-missing-wf.cwl tests/record-secondaryFiles-job.yml
[1;30mERROR[0m [31mException on step 'step1'[0m
[1;30mERROR[0m [31m[step step1] Cannot make job: tests/record-in-secondaryFiles.cwl:10:11: Missing required secondary file 'A.s2' from file object: {
tests/record-in-secondaryFiles.cwl:10:11: "class": "File",
tests/record-in-secondaryFiles.cwl:10:11: "location": "file:///conformance/cwl-v1.2-1.2.1_proposed/tests/rec/A",
tests/record-in-secondaryFiles.cwl:10:11: "size": 0,
tests/record-in-secondaryFiles.cwl:10:11: "basename": "A",
tests/record-in-secondaryFiles.cwl:10:11: "nameroot": "A",
tests/record-in-secondaryFiles.cwl:10:11: "nameext": "",
tests/record-in-secondaryFiles.cwl:10:11: "secondaryFiles": []
tests/record-in-secondaryFiles.cwl:10:11: }[0m
[1;30mWARNING[0m [33mFinal process status is permanentFail[0m
Test [208/378] input_records_file_entry_with_format: Test format on anonymous record fields
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpev17g96a --quiet tests/record-in-format.cwl tests/record-format-job.yml
Test [209/378] input_records_file_entry_with_format_and_bad_regular_input_file_format: Test file format checking on parameter
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp8k8iy0fa --quiet tests/record-in-format.cwl tests/record-format-job2.yml
[1;30mERROR[0m [31mWorkflow error, try again with --debug for more information:
Expected value of 'regular_input' to have format 'http://example.com/format1' but
File has an incompatible format: {
"class": "File",
"location": "file:///conformance/cwl-v1.2-1.2.1_proposed/tests/rec/D",
"format": "http://example.com/formatZ",
"size": 0,
"basename": "D",
"nameroot": "D",
"nameext": ""
}[0m
Test [210/378] input_records_file_entry_with_format_and_bad_entry_file_format: Test file format checking on record field
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp5pghej8m --quiet tests/record-in-format.cwl tests/record-format-job3.yml
[1;30mERROR[0m [31mWorkflow error, try again with --debug for more information:
Expected value of 'f1' to have format 'http://example.com/format1' but
File has an incompatible format: {
"class": "File",
"location": "file:///conformance/cwl-v1.2-1.2.1_proposed/tests/rec/A",
"format": "http://example.com/formatZ",
"size": 0,
"basename": "A",
"nameroot": "A",
"nameext": ""
}[0m
Test [211/378] input_records_file_entry_with_format_and_bad_entry_array_file_format: Test file format checking on array item
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmph1b8pysu --quiet tests/record-in-format.cwl tests/record-format-job4.yml
[1;30mERROR[0m [31mUnhandled error, try again with --debug for more information:
'name'[0m
Test [212/378] record_output_file_entry_format: Test format on output record fields
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp0yza7izj --quiet tests/record-out-format.cwl tests/record-secondaryFiles-job.yml
Test [213/378] workflow_input_inputBinding_loadContents: Test WorkflowInputParameter.inputBinding.loadContents
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpxu8cl1pn --quiet tests/wf-loadContents.cwl tests/wf-loadContents-job.yml
Test [214/378] workflow_input_loadContents_without_inputBinding: Test WorkflowInputParameter.loadContents
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmproha8ltu --quiet tests/wf-loadContents2.cwl tests/wf-loadContents-job.yml
Test [215/378] expression_tool_input_loadContents: Test loadContents on InputParameter.loadContents (expression)
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmptbn7gvzv --quiet tests/wf-loadContents3.cwl tests/wf-loadContents-job.yml
Test [216/378] workflow_step_in_loadContents: Test WorkflowStepInput.loadContents
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp71tci4ik --quiet tests/wf-loadContents4.cwl tests/wf-loadContents-job.yml
Test [217/378] timelimit_basic: Test that job fails when exceeding time limit
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpcnp0mo0s --quiet tests/timelimit.cwl tests/empty.json
Test 217 failed: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpcnp0mo0s --quiet tests/timelimit.cwl tests/empty.json
Test that job fails when exceeding time limit
Returned zero but it should be non-zero
Test [218/378] timelimit_invalid: Test invalid time limit value
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmplwezl48n --quiet tests/timelimit2.cwl tests/empty.json
[1;30mERROR[0m [31mInput object failed validation:
tests/timelimit2.cwl:7:5: timelimit must be an integer >= 0, got: -1[0m
Test [219/378] timelimit_zero_unlimited: Test zero timelimit means no limit
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmps5ydfp4z --quiet tests/timelimit3.cwl tests/empty.json
Test [220/378] timelimit_from_expression: Test expression in time limit
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp3t5s81_e --quiet tests/timelimit4.cwl tests/empty.json
Test 220 failed: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp3t5s81_e --quiet tests/timelimit4.cwl tests/empty.json
Test expression in time limit
Returned zero but it should be non-zero
Test [221/378] timelimit_expressiontool: Test timelimit in expressiontool is ignored
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp090su6uv --quiet tests/timelimit5.cwl tests/empty.json
Test [222/378] timelimit_basic_wf: Test that tool in workflow fails when exceeding time limit
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpzcvrgjos --quiet tests/timelimit-wf.cwl tests/empty.json
Test 222 failed: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpzcvrgjos --quiet tests/timelimit-wf.cwl tests/empty.json
Test that tool in workflow fails when exceeding time limit
Returned zero but it should be non-zero
Test [223/378] timelimit_invalid_wf: Test that workflow level time limit is not applied to workflow execution time
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp_f_w4oud --quiet tests/timelimit2-wf.cwl tests/empty.json
Test [224/378] timelimit_zero_unlimited_wf: Test zero timelimit means no limit in workflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpzscoiy1u --quiet tests/timelimit3-wf.cwl tests/empty.json
Test [225/378] timelimit_from_expression_wf: Test expression in time limit in workflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp4bwvhzd5 --quiet tests/timelimit4-wf.cwl tests/empty.json
Test 225 failed: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp4bwvhzd5 --quiet tests/timelimit4-wf.cwl tests/empty.json
Test expression in time limit in workflow
Returned zero but it should be non-zero
Test [226/378] networkaccess: Test networkaccess enabled
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmppl4vr2ee --quiet tests/networkaccess.cwl tests/empty.json
Test [227/378] networkaccess_disabled: Test networkaccess is disabled by default
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpm9wp4ces --quiet tests/networkaccess2.cwl tests/empty.json
Test 227 failed: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpm9wp4ces --quiet tests/networkaccess2.cwl tests/empty.json
Test networkaccess is disabled by default
Returned zero but it should be non-zero
Test [228/378] initial_work_dir_for_null_and_arrays: Test null and array input in InitialWorkDirRequirement
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpvhlkh005 --quiet tests/stage-array.cwl tests/stage-array-job.json
Test [229/378] initial_work_dir_for_array_dirs: Test array of directories InitialWorkDirRequirement
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpl9y8xkqz --quiet tests/stage-array-dirs.cwl tests/stage-array-dirs-job.yml
Test 229 failed: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpl9y8xkqz --quiet tests/stage-array-dirs.cwl tests/stage-array-dirs-job.yml
Test array of directories InitialWorkDirRequirement
Compare failure expected: {
"output": [
{
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"class": "File",
"location": "a",
"size": 0
},
{
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"class": "File",
"location": "B",
"size": 0
}
]
}
got: {
"output": []
}
caused by: failed comparison for key 'output': expected: [
{
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"class": "File",
"location": "a",
"size": 0
},
{
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"class": "File",
"location": "B",
"size": 0
}
]
got: []
caused by: lengths don't match
Test [230/378] cwl_requirements_addition: Test requirements in input document via EnvVarRequirement
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpeotz4m85 --quiet tests/env-tool3.cwl tests/env-job3.yaml
Test [231/378] cwl_requirements_override_expression: Test conflicting requirements in input document via EnvVarRequirement and expression
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpzlh_op1t --quiet tests/env-tool4.cwl tests/env-job3.yaml
Test [232/378] cwl_requirements_override_static: Test conflicting requirements in input document via EnvVarRequirement
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp521cktsn --quiet tests/env-tool3.cwl tests/env-job4.yaml
Test [233/378] initial_workdir_output_glob: Test full path glob output of InitialWorkDir
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwg7fvp6f --quiet tests/initialworkdir-glob-fullpath.cwl tests/initialworkdirrequirement-docker-out-job.json
Test [234/378] glob_outside_outputs_fails: Test fail trying to glob outside output directory
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpfbr7lm18 --quiet tests/glob-path-error.cwl tests/empty.json
[1;30mERROR[0m [31mFound a queued exception, canceling outstanding futures[0m
[1;30mERROR[0m [31mWaiting for canceled futures to finish[0m
[1;30mERROR[0m [31mWorkflow error, try again with --debug for more information:
("Error collecting output for parameter 'OUTPUT': tests/glob-path-error.cwl:17:7: glob patterns must
not start with
'/'", {})[0m
Test [235/378] illegal_symlink: symlink to file outside of working directory should NOT be retrieved
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmprra75iod --quiet tests/symlink-illegal.cwl tests/empty.json
[1;30mERROR[0m [31mFound a queued exception, canceling outstanding futures[0m
[1;30mERROR[0m [31mWaiting for canceled futures to finish[0m
[1;30mERROR[0m [31mWorkflow error, try again with --debug for more information:
Error validating output record. Does not exist or is not a Directory: 'file:///output/68kp7qap/symlink.txt'
in {
"output_file": {
"location": "file:///output/68kp7qap/symlink.txt",
"basename": "symlink.txt",
"nameroot": "symlink",
"nameext": ".txt",
"class": "Directory"
}
}[0m
Test [236/378] legal_symlink: symlink to file inside of working directory should be retrieved
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpv8q58idk --quiet tests/symlink-legal.cwl tests/empty.json
Test [237/378] modify_file_content: inplace update has side effect on file content
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpzzdnbkjy --quiet tests/inp_update_wf.cwl tests/empty.json
[1;30mWARNING[0m [33mWorkflow checker warning:
tests/inp_update_wf.cwl:26:7: 'wait' is not an input parameter of
file:///conformance/cwl-v1.2-1.2.1_proposed/tests/parseInt-tool.cwl,
expected file1[0m
Test 237 failed: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpzzdnbkjy --quiet tests/inp_update_wf.cwl tests/empty.json
inplace update has side effect on file content
Compare failure expected: {
"a": 4,
"b": 4
}
got: {
"a": 4,
"b": null
}
caused by: failed comparison for key 'b': expected: 4
got: null
Test [238/378] modify_directory_content: inplace update has side effect on directory content
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpp6jhk6tx --quiet tests/inpdir_update_wf.cwl tests/empty.json
Test 238 failed: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpp6jhk6tx --quiet tests/inpdir_update_wf.cwl tests/empty.json
inplace update has side effect on directory content
Compare failure expected: {
"a": [
{
"basename": "blurb",
"class": "File",
"location": "blurb"
}
],
"b": [
{
"basename": "blurb",
"class": "File",
"location": "blurb"
}
]
}