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results-v1.2.txt
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The `id` field with integer is deprecated. Use string identifier instead.
The `id` field with integer is deprecated. Use string identifier instead.
The `id` field with integer is deprecated. Use string identifier instead.
The `id` field with integer is deprecated. Use string identifier instead.
The `id` field with integer is deprecated. Use string identifier instead.
The `id` field with integer is deprecated. Use string identifier instead.
The `id` field with integer is deprecated. Use string identifier instead.
The `id` field with integer is deprecated. Use string identifier instead.
The `id` field with integer is deprecated. Use string identifier instead.
The `id` field is missing.
The `id` field is missing.
The `id` field is missing.
The `id` field is missing.
The `id` field is missing.
The `id` field is missing.
The `id` field is missing.
The `id` field is missing.
The `id` field is missing.
The `id` field is missing.
Test [1/336] cl_basic_generation: General test of command line generation
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp3jpl1jes --quiet tests/bwa-mem-tool.cwl tests/bwa-mem-job.json
Test [2/336] nested_prefixes_arrays: Test nested prefixes with arrays
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp43lwux51 --quiet tests/binding-test.cwl tests/bwa-mem-job.json
Test [3/336] nested_cl_bindings: Test nested command line bindings
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp2lm41272 --quiet tests/tmap-tool.cwl tests/tmap-job.json
Test [4/336] 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/tmplr9takw3 --quiet tests/cat1-testcli.cwl tests/cat-job.json
Test [5/336] 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/tmpbt__9e4q --quiet tests/cat1-testcli.cwl tests/cat-n-job.json
Test [6/336] initworkdir_expreng_requirements: Test InitialWorkDirRequirement ExpressionEngineRequirement.engineConfig feature
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwiust2ou --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 [7/336] 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/tmpxusw3uos --quiet tests/cat3-tool.cwl tests/cat-job.json
Test [8/336] 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/tmp2h7lz502 --quiet tests/cat3-tool-shortcut.cwl tests/cat-job.json
Test [9/336] 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/tmpsb44tod2 --quiet tests/cat3-tool-mediumcut.cwl tests/cat-job.json
Test [10/336] stderr_redirect: Test command line with stderr redirection
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpbh4qu5sd --quiet tests/stderr.cwl tests/empty.json
Test [11/336] 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/tmpi8i5t8w4 --quiet tests/stderr-shortcut.cwl tests/empty.json
Test [12/336] 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/tmp4mcnke92 --quiet tests/stderr-mediumcut.cwl tests/empty.json
Test [13/336] 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/tmp_7pgg8zt --quiet tests/cat4-tool.cwl tests/cat-job.json
Test [14/336] expression_any: Test default usage of Any in expressions.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpptehd4kh --quiet tests/null-expression1-tool.cwl tests/empty.json
Test [15/336] 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/tmpfcw35h8n --quiet tests/null-expression1-tool.cwl tests/null-expression1-job.json
Test [16/336] 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/tmppv2hc80x --quiet tests/null-expression1-tool.cwl tests/null-expression2-job.json
Test [17/336] 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/tmpm5560ode --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 [18/336] 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/tmpmx75vn5b --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 [19/336] 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/tmp4rxbll7v --quiet tests/null-expression2-tool.cwl tests/null-expression2-job.json
Test [20/336] any_outputSource_compatibility: Testing Any type compatibility in outputSource
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpzcr8b6ug --quiet tests/any-type-compat.cwl tests/any-type-job.json
Test [21/336] 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/tmpygep2pc_ --quiet tests/cat-tool.cwl tests/cat-job.json
Test [22/336] expression_parseint: Test ExpressionTool with Javascript engine
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpm606frhl --quiet tests/parseInt-tool.cwl tests/parseInt-job.json
Test [23/336] expression_outputEval: Test outputEval to transform output
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp3jv460nx --quiet tests/wc2-tool.cwl tests/wc-job.json
Test [24/336] 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/tmpkwir9k9m --quiet tests/count-lines1-wf.cwl tests/wc-job.json
Test [25/336] 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/tmpsml9z970 --quiet tests/count-lines2-wf.cwl tests/wc-job.json
Test [26/336] 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/tmpm6rxk67o --quiet tests/count-lines3-wf.cwl tests/count-lines3-job.json
Test [27/336] 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/tmp6_avqgk7 --quiet tests/count-lines4-wf.cwl tests/count-lines4-job.json
Test [28/336] 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/tmpaznwshe4 --quiet tests/count-lines6-wf.cwl tests/count-lines6-job.json
Test [29/336] 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/tmpoof8zxnh --quiet tests/count-lines7-wf.cwl tests/count-lines6-job.json
Test [30/336] 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/tmpl6tgu6gx --quiet tests/count-lines13-wf.cwl tests/count-lines4-job.json
Test [31/336] wf_wc_nomultiple: 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/tmpnsn5k97a --quiet tests/count-lines19-wf.cwl tests/count-lines4-job.json
Test [32/336] 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/tmpmhiug9d1 --quiet tests/count-lines5-wf.cwl tests/empty.json
Test [33/336] 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/tmp2zusgcvn --quiet tests/count-lines5-wf.cwl tests/wc-job.json
Test [34/336] 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/tmp_n_ao3pi --quiet tests/echo-wf-default.cwl tests/empty.json
Test [35/336] envvar_req: Test EnvVarRequirement
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmphii2d361 --quiet tests/env-tool1.cwl tests/env-job.json
Test [36/336] 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/tmp31rus9mk --quiet tests/scatter-wf1.cwl tests/scatter-job1.json
Test [37/336] 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/tmpm_vyz9yh --quiet tests/scatter-wf2.cwl tests/scatter-job2.json
Test [38/336] 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/tmprtefgl3n --quiet tests/scatter-wf3.cwl#main tests/scatter-job2.json
Test [39/336] 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/tmpj4w01_65 --quiet tests/scatter-wf4.cwl#main tests/scatter-job2.json
Test [40/336] 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/tmpaow3ug68 --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 [41/336] 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/tmpn58l43vx --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 [42/336] 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/tmpugv_pt0h --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 [43/336] 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/tmpsayu4awr --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 [44/336] 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/tmpo4pu3pj0 --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 [45/336] any_input_param: Test Any type input parameter
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpxr5bpm41 --quiet tests/echo-tool.cwl tests/env-job.json
Test [46/336] nested_workflow: Test nested workflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwgnbwygl --quiet tests/count-lines8-wf.cwl tests/wc-job.json
Test [47/336] requirement_priority: Test requirement priority
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpphydqmz2 --quiet tests/env-wf1.cwl tests/env-job.json
Test [48/336] requirement_override_hints: Test requirements override hints
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpgv1_6rt4 --quiet tests/env-wf2.cwl tests/env-job.json
Test [49/336] requirement_workflow_steps: Test requirements on workflow steps
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpx4lhamyw --quiet tests/env-wf3.cwl tests/env-job.json
Test [50/336] 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/tmp2y52jg91 --quiet tests/count-lines9-wf.cwl tests/empty.json
Test [51/336] 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/tmp39osk55x --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 [52/336] 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/tmpvyr740yo --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 [53/336] 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/tmpkqvmooyn --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 [54/336] wf_simple: Test simple workflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpsmv0fzpm --quiet tests/revsort.cwl tests/revsort-job.json
Test [55/336] hints_unknown_ignored: Test unknown hints are ignored.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpq2se2pq0 --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 [56/336] 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/tmp81s3q0cj --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 [57/336] rename: Test InitialWorkDirRequirement with expression in filename.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp5m9xn_8c --quiet tests/rename.cwl tests/rename-job.json
Test [58/336] 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/tmpy0gam_ut --quiet tests/iwdr-entry.cwl tests/string-job.json
Test [59/336] inline_expressions: Test inline expressions
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpdtl7ud2a --quiet tests/wc4-tool.cwl tests/wc-job.json
Test [60/336] 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/tmp_hqjkg15 --quiet tests/schemadef-tool.cwl tests/schemadef-job.json
Test [61/336] 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/tmp0c30_7c2 --quiet tests/schemadef-wf.cwl tests/schemadef-job.json
Test [62/336] 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/tmpul4ana0c --quiet tests/params.cwl tests/empty.json
Test [63/336] 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/tmptz88k6xq --quiet tests/params2.cwl tests/empty.json
Test [64/336] metadata: Test metadata
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpyj4bybgv --quiet tests/metadata.cwl tests/cat-job.json
Test [65/336] format_checking: Test simple format checking.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpin_pb65w --quiet tests/formattest.cwl tests/formattest-job.json
Test [66/336] 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/tmp1ek271fp --quiet tests/formattest2.cwl tests/formattest2-job.json
Test [67/336] 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/tmpl8hkbile --quiet tests/formattest3.cwl tests/formattest2-job.json
Test [68/336] 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/tmplnp4_my0 --quiet tests/optional-output.cwl tests/cat-job.json
Test [69/336] 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/tmpeioyez2r --quiet tests/vf-concat.cwl tests/empty.json
Test [70/336] 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/tmp8pg8t95l --quiet tests/vf-concat.cwl tests/cat-job.json
Test [71/336] valuefrom_wf_step: Test valueFrom on workflow step.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp1ex0lb_1 --quiet tests/step-valuefrom-wf.cwl tests/step-valuefrom-wf.json
Test [72/336] 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/tmpcmuhuo28 --quiet tests/step-valuefrom2-wf.cwl tests/step-valuefrom-job.json
Test [73/336] 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/tmpt80rae9k --quiet tests/step-valuefrom3-wf.cwl tests/step-valuefrom-job.json
Test [74/336] record_output_binding: Test record type output binding.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpy28j4fvb --quiet tests/record-output.cwl tests/record-output-job.json
Test [75/336] 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/tmptyj_tpkl --quiet tests/test-cwl-out.cwl tests/empty.json
Test [76/336] 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/tmpm9wshay2 --quiet tests/test-cwl-out2.cwl tests/empty.json
Test [77/336] 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/tmpqqecdr6h --quiet tests/glob-expr-list.cwl tests/abc.json
Test [78/336] 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/tmpp49pfe83 --quiet tests/scatter-valuefrom-wf1.cwl tests/scatter-valuefrom-job1.json
Test [79/336] 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/tmpi10kmun1 --quiet tests/scatter-valuefrom-wf2.cwl tests/scatter-valuefrom-job2.json
Test [80/336] 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/tmp8ly_3ijo --quiet tests/scatter-valuefrom-wf3.cwl#main tests/scatter-valuefrom-job2.json
Test [81/336] 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/tmp5tli5o1x --quiet tests/scatter-valuefrom-wf4.cwl#main tests/scatter-valuefrom-job2.json
Test [82/336] 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/tmp911k169b --quiet tests/scatter-valuefrom-wf5.cwl tests/scatter-valuefrom-job1.json
Test [83/336] 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/tmp8a_dee4h --quiet tests/scatter-valuefrom-wf6.cwl tests/scatter-valuefrom-job3.json
Test [84/336] 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/tmp8lang0ta --quiet tests/conflict-wf.cwl#collision tests/conflict-job.json
Test [85/336] 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/tmpw8bn0h0d --quiet tests/dir.cwl tests/dir-job.yml
Test [86/336] directory_input_docker: Test directory input in Docker
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpd46jf319 --quiet tests/dir2.cwl tests/dir-job.yml
Test [87/336] directory_output: Test directory output
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpo3rrj6p3 --quiet tests/dir3.cwl tests/dir3-job.yml
Test [88/336] directory_secondaryfiles: Test directories in secondaryFiles
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp_h762hs3 --quiet tests/dir4.cwl tests/dir4-job.yml
Test [89/336] dynamic_initial_workdir: Test dynamic initial work dir
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpksrgk03q --quiet tests/dir5.cwl tests/dir-job.yml
Test [90/336] writable_stagedfiles: Test writable staged files.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpljdqbj_2 --quiet tests/stagefile.cwl tests/stagefile-job.yml
Test [91/336] input_file_literal: Test file literal as input
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmphy3bfbrd --quiet tests/cat3-tool.cwl tests/file-literal.yml
Test [92/336] initial_workdir_expr: Test expression in InitialWorkDir listing
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpuosi9a9r --quiet tests/linkfile.cwl tests/arguments-job.yml
Test [93/336] 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/tmpj1iqy8ew --quiet tests/nameroot.cwl tests/wc-job.json
Test [94/336] input_dir_inputbinding: Test directory input with inputBinding
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpeh_irvbq --quiet tests/dir6.cwl tests/dir-job.yml
Test [95/336] 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/tmp_yq5wks4 --quiet tests/nested-array.cwl tests/nested-array-job.yml
Test [96/336] 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/tmpbjg4kkvx --quiet tests/envvar.cwl tests/empty.json
Test [97/336] 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/tmpjfyty7y3 --quiet tests/envvar2.cwl tests/empty.json
Test [98/336] 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/tmpb2lv1obc --quiet tests/js-expr-req-wf.cwl#wf tests/empty.json
Test [99/336] initial_workdir_output: Test output of InitialWorkDir
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmps4pj2i1s --quiet tests/initialworkdirrequirement-docker-out.cwl tests/initialworkdirrequirement-docker-out-job.json
Test [100/336] embedded_subworkflow: Test embedded subworkflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpcys79ug3 --quiet tests/count-lines10-wf.cwl tests/wc-job.json
Test [101/336] 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/tmp4m2me1av --quiet tests/docker-array-secondaryfiles.cwl tests/docker-array-secondaryfiles-job.json
Test [102/336] 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/tmpftac4gmf --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-v1.2-1.2.0/tests/ref.fasta",
"size": 12010,
"basename": "ref.fasta",
"nameroot": "ref",
"nameext": ".fasta",
"secondaryFiles": [
{
"location": "file:///conformance/cwl-v1.2-1.2.0/tests/ref.fasta.fai",
"basename": "ref.fasta.fai",
"class": "File"
}
]
}[0m
Test [103/336] 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/tmpw4jle0qy --quiet tests/dir7.cwl tests/dir7.yml
Test [104/336] 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/tmpwfd0m9l0 --quiet tests/file-literal-ex.cwl tests/empty.json
Test [105/336] dockeroutputdir: Test dockerOutputDirectory
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp9yu3yelc --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 [106/336] hints_import: Test hints with $import
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp9wqqqxgj --quiet tests/imported-hint.cwl tests/empty.json
Test [107/336] 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/tmp9_mrfp2n --quiet tests/default_path.cwl tests/default_path_job.yml
Test [108/336] 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/tmp9gjjh69h --quiet tests/inline-js.cwl tests/empty.json
Test [109/336] 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/tmp_qbdk3tf --quiet tests/recursive-input-directory.cwl tests/recursive-input-directory.yml
Test [110/336] 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/tmpreithux9 --quiet tests/null-defined.cwl tests/empty.json
Test [111/336] 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/tmpc6w48m40 --quiet tests/null-defined.cwl tests/cat-job.json
Test [112/336] wf_compound_doc: Test compound workflow document
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpzeofl9kt --quiet tests/revsort-packed.cwl#main tests/revsort-job.json
Test [113/336] 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/tmpp8j6iwo6 --quiet tests/basename-fields-test.cwl tests/basename-fields-job.yml
Test [114/336] 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/tmp_jmkf_b6 --quiet tests/initialwork-path.cwl tests/wc-job.json
Test [115/336] 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/tmprtl0ysmt --quiet tests/count-lines12-wf.cwl tests/count-lines6-job.json
Test [116/336] 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/tmphfjnk3vy --quiet tests/sum-wf.cwl tests/sum-job.json
Test [117/336] shelldir_notinterpreted: Test that shell directives are not interpreted.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpgvo5frc0 --quiet tests/shellchar.cwl tests/empty.json
Test [118/336] shelldir_quoted: Test that shell directives are quoted.
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpen97duvr --quiet tests/shellchar2.cwl tests/empty.json
Test [119/336] 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/tmpl57kf8wy --quiet tests/writable-dir.cwl tests/empty.json
Test [120/336] 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/tmpc0p291_s --quiet tests/writable-dir-docker.cwl tests/empty.json
Test [121/336] dynamic_resreq_inputs: Test dynamic resource reqs referencing inputs
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpqh4g655b --quiet tests/dynresreq.cwl tests/dynresreq-job.yaml
Test [122/336] 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/tmp4xzmr634 --quiet tests/cat3-nodocker.cwl tests/file-literal.yml
Test [123/336] 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/tmpoo7xxgyl --quiet tests/glob_test.cwl tests/empty.json
Test [124/336] 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/tmppkeaeouq --quiet tests/iwdr_with_nested_dirs.cwl tests/empty.json
Test [125/336] 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/tmpp6mggmqu --quiet tests/bool-empty-inputbinding.cwl tests/bool-empty-inputbinding-job.json
Test [126/336] 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/tmpf3imekt3 --quiet tests/stage-unprovided-file.cwl tests/empty.json
Test [127/336] success_codes: Test successCodes
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp7_u640un --quiet tests/exit-success.cwl tests/empty.json
Test [128/336] 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/tmp54l1ed8w --quiet tests/dynresreq-workflow.cwl tests/dynresreq-job.yaml
Test [129/336] 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/tmpgbs6ugti --quiet tests/empty-array-input.cwl tests/empty-array-job.json
Test [130/336] 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/tmpb7vxt1p8 --quiet tests/steplevel-resreq.cwl tests/empty.json
Test [131/336] 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/tmpl5q5xzc0 --quiet tests/valueFrom-constant.cwl tests/array-of-strings-job.yml
Test [132/336] 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/tmpwyrh2qqm --quiet tests/dynresreq-dir.cwl tests/dynresreq-dir-job.yaml
Test [133/336] 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/tmpby46_fwh --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-v1.2-1.2.0/tests/echo-tool.cwl, expected in[0m
Test [134/336] 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/tmpt6bv1fq5 --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-v1.2-1.2.0/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 [135/336] env_home_tmpdir_docker: 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/tmpir8eosw9 --quiet tests/envvar3.cwl tests/empty.json
Test [136/336] 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/tmp2bu8sikn --quiet tests/scatter-valuefrom-inputs-wf1.cwl tests/scatter-valuefrom-job1.json
Test [137/336] packed_import_schema: SchemaDefRequirement with $import, and packed
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpxp_z6rky --quiet tests/import_schema-def_packed.cwl tests/import_schema-def_job.yml
Test [138/336] 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/tmp0xwdm4m9 --quiet tests/dir4.cwl tests/dir4-subdir-1-job.yml
Test [139/336] 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/tmpuie5ftuf --quiet tests/dir4.cwl tests/dir4-subdir-2-job.yml
Test [140/336] 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/tmpre2kn7jw --quiet tests/count-lines18-wf.cwl tests/count-lines3-job.json
Test [141/336] 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/tmpg54begp1 --quiet tests/count-lines14-wf.cwl tests/count-lines4-job.json
Test [142/336] workflow_embedded_subworkflow_embedded_subsubworkflow: Test twice nested subworkflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp03_qvlcb --quiet tests/count-lines15-wf.cwl tests/wc-job.json
Test [143/336] 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/tmpi5ugf2z2 --quiet tests/count-lines16-wf.cwl tests/wc-job.json
Test [144/336] 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/tmpp5iojvlv --quiet tests/count-lines17-wf.cwl tests/wc-job.json
Test [145/336] 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/tmpr2m82sjo --quiet tests/record-output-wf.cwl tests/record-output-job.json
Test [146/336] workflow_integer_input: Test integer workflow input and outputs
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpcxut20ta --quiet tests/io-int-wf.cwl tests/io-int.json
Test [147/336] 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/tmpmqstoy7d --quiet tests/io-int-optional-wf.cwl tests/io-int.json
Test [148/336] 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/tmp2tll82n4 --quiet tests/io-int-optional-wf.cwl tests/empty.json
Test [149/336] 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/tmp5yc94smr --quiet tests/io-int-default-wf.cwl tests/io-int.json
Test [150/336] 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/tmpn4pwaprm --quiet tests/io-int-default-wf.cwl tests/empty.json
Test [151/336] 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/tmpjk7c8l3p --quiet tests/io-int-default-tool-and-wf.cwl tests/empty.json
Test [152/336] 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/tmp0njv1hfy --quiet tests/io-file-default-wf.cwl tests/empty.json
Test [153/336] 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/tmpw_c6r9cr --quiet tests/io-file-default-wf.cwl tests/default_path_job.yml
Test [154/336] 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/tmp6rjnnd3m --quiet tests/io-file-or-files.cwl tests/job-input-array-one-empty-file.json
Test [155/336] 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/tmp04_if_z8 --quiet tests/io-file-or-files.cwl tests/job-input-array-few-files.json
Test [156/336] 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/tmpy9htsqdi --quiet tests/io-file-or-files.cwl tests/job-input-one-file.json
Test [157/336] 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/tmpnvc7m2c3 --quiet tests/io-file-or-files.cwl tests/job-input-null.json
Test [158/336] 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/tmp1rpqd997 --quiet tests/io-any-1.cwl tests/io-any-int.json
Test [159/336] 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/tmpalqqo8tj --quiet tests/io-any-1.cwl tests/io-any-string.json
Test [160/336] 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/tmpm8_ah0_5 --quiet tests/io-any-1.cwl tests/io-any-file.json
Test [161/336] 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/tmpi8rnezhf --quiet tests/io-any-1.cwl tests/io-any-array.json
Test [162/336] 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/tmp_1l33n8h --quiet tests/io-any-1.cwl tests/io-any-record.json
Test [163/336] 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/tmpx7wafik6 --quiet tests/io-any-wf-1.cwl tests/io-any-int.json
Test [164/336] 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/tmpwgor9c_y --quiet tests/io-any-wf-1.cwl tests/io-any-string.json
Test [165/336] 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/tmp5ew15hl5 --quiet tests/io-any-wf-1.cwl tests/io-any-file.json
Test [166/336] 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/tmp0vrprqpl --quiet tests/io-any-wf-1.cwl tests/io-any-array.json
Test [167/336] 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/tmphjfzcaod --quiet tests/io-any-wf-1.cwl tests/io-any-record.json
Test [168/336] 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/tmp536fb5b9 --quiet tests/io-union-input-default-wf.cwl tests/empty.json
Test [169/336] 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/tmpt7hrp48w --quiet tests/io-union-input-default-wf.cwl tests/io-any-file.json
Test [170/336] 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/tmpbojd2x98 --quiet tests/step-valuefrom4-wf.cwl tests/empty.json
Test [171/336] 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/tmpf7i6zucy --quiet tests/step-valuefrom5-wf.cwl tests/wc-job.json
Test [172/336] 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/tmpoqozec8p --quiet tests/output-arrays-int.cwl tests/output-arrays-int-job.json
Test [173/336] 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/tmp6htzechi --quiet tests/output-arrays-int-wf.cwl tests/output-arrays-int-job.json
Test [174/336] 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/tmpt3e1g8aw --quiet tests/output-arrays-file-wf.cwl tests/output-arrays-file-job.json
Test [175/336] docker_entrypoint: Test Docker ENTRYPOINT usage
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpo1lmmaz1 --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 175 failed: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpo1lmmaz1 --quiet tests/docker-run-cmd.cwl tests/empty.json
Test Docker ENTRYPOINT usage
Returned non-zero
Test [176/336] 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/tmpozf91zw7 --quiet tests/size-expression-tool.cwl tests/job-input-array-one-empty-file.json
Test [177/336] 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/tmpc6vrred1 --quiet tests/size-expression-tool.cwl tests/job-input-array-few-files.json
Test [178/336] 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/tmp0e_mr685 --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 [179/336] 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/tmpn94r8k4f --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 [180/336] 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/tmpqk3t10dj --quiet tests/count-lines9-wf-noET.cwl tests/empty.json
Test [181/336] 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/tmpipnkwdsg --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 [182/336] nested_workflow_noexp: Test nested workflow, without ExpressionTool
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpy6hjnrfb --quiet tests/count-lines8-wf-noET.cwl tests/wc-job.json
Test [183/336] 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/tmpdmdmtfdp --quiet tests/sum-wf-noET.cwl tests/sum-job.json
Test [184/336] 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/tmp9v_t_81n --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 [185/336] 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/tmpi6dxexxg --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 [186/336] 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/tmpsxtf7eio --quiet tests/dynresreq-workflow-inputdefault.cwl tests/empty.json
Test [187/336] 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/tmpg2kc57iw --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 [188/336] 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/tmpxnyyt840 --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 [189/336] 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/tmpeh4_1jbl --quiet tests/count-lines11-null-step-wf.cwl tests/empty.json
Test [190/336] 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/tmpz5phiwp3 --quiet tests/count-lines11-null-step-wf-noET.cwl tests/empty.json
Test [191/336] 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/tmpej304maq --quiet tests/cat-from-dir.cwl tests/cat-from-dir-job.yaml
Test [192/336] 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/tmppro07znf --quiet tests/cat-from-dir.cwl tests/cat-from-dir-with-literal-file.yaml
Test [193/336] 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/tmp9f0j__9r --quiet tests/cat3-from-dir.cwl tests/cat-from-dir-with-literal-file.yaml
Test [194/336] no_inputs_commandlinetool: Test CommandLineTool without inputs
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmppyiw1o3k --quiet tests/no-inputs-tool.cwl
Test [195/336] no_outputs_commandlinetool: Test CommandLineTool without outputs
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp317rmrkt --quiet tests/no-outputs-tool.cwl tests/cat-job.json
Test [196/336] no_inputs_workflow: Test Workflow without inputs
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp4gwlgp42 --quiet tests/no-inputs-wf.cwl
Test [197/336] no_outputs_workflow: Test Workflow without outputs
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpt820_c0o --quiet tests/no-outputs-wf.cwl tests/cat-job.json
Test [198/336] 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/tmp8s9l4u11 --quiet tests/anon_enum_inside_array.cwl tests/anon_enum_inside_array.yml
Test [199/336] 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/tmp_arnka7l --quiet tests/anon_enum_inside_array_inside_schemadef.cwl tests/anon_enum_inside_array_inside_schemadef.yml
Test [200/336] 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/tmpz5xip9c7 --quiet tests/cat-tool-shortcut.cwl tests/wc-job.json
Test [201/336] 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/tmpnxponl5x --quiet tests/record-in-secondaryFiles.cwl tests/record-secondaryFiles-job.yml
Test [202/336] 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/tmp4ngcup1x --quiet tests/record-sd-secondaryFiles.cwl tests/record-secondaryFiles-job.yml
Test [203/336] 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/tmpn3tbrv2a --quiet tests/record-out-secondaryFiles.cwl tests/empty.json
Test [204/336] secondary_files_workflow_propagation: Test secondaryFiles propagation through workflow
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp_3wuwqfl --quiet tests/record-in-secondaryFiles-wf.cwl tests/record-secondaryFiles-job.yml
Test [205/336] secondary_files_missing: Test checking when secondaryFiles are missing
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpebwk5i0r --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-v1.2-1.2.0/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 [206/336] 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/tmpc5g_bago --quiet tests/record-in-format.cwl tests/record-format-job.yml
Test [207/336] 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/tmp66zrwjc7 --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-v1.2-1.2.0/tests/rec/D",
"format": "http://example.com/formatZ",
"size": 0,
"basename": "D",
"nameroot": "D",
"nameext": ""
}[0m
Test [208/336] 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/tmpyn7e3znb --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-v1.2-1.2.0/tests/rec/A",
"format": "http://example.com/formatZ",
"size": 0,
"basename": "A",
"nameroot": "A",
"nameext": ""
}[0m
Test [209/336] 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/tmpm5y1mlt6 --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 [210/336] 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/tmpje7vn0e4 --quiet tests/record-out-format.cwl tests/record-secondaryFiles-job.yml
Test [211/336] workflow_input_inputBinding_loadContents: Test WorkflowInputParameter.inputBinding.loadContents
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp_opkgxvy --quiet tests/wf-loadContents.cwl tests/wf-loadContents-job.yml
Test [212/336] workflow_input_loadContents_without_inputBinding: Test WorkflowInputParameter.loadContents
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpeuz_ibip --quiet tests/wf-loadContents2.cwl tests/wf-loadContents-job.yml
Test [213/336] 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/tmpecxc2_x7 --quiet tests/wf-loadContents3.cwl tests/wf-loadContents-job.yml
Test [214/336] workflow_step_in_loadContents: Test WorkflowStepInput.loadContents
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp3l0wbp7t --quiet tests/wf-loadContents4.cwl tests/wf-loadContents-job.yml
Test [215/336] 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/tmpq1rw9ap0 --quiet tests/timelimit.cwl tests/empty.json
Test 215 failed: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpq1rw9ap0 --quiet tests/timelimit.cwl tests/empty.json
Test that job fails when exceeding time limit
Returned zero but it should be non-zero
Test [216/336] timelimit_invalid: Test invalid time limit value
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwhj1iu5u --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 [217/336] timelimit_zero_unlimited: Test zero timelimit means no limit
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpowonaj0u --quiet tests/timelimit3.cwl tests/empty.json
Test [218/336] timelimit_from_expression: Test expression in time limit
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwh9l5tru --quiet tests/timelimit4.cwl tests/empty.json
Test 218 failed: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwh9l5tru --quiet tests/timelimit4.cwl tests/empty.json
Test expression in time limit
Returned zero but it should be non-zero
Test [219/336] timelimit_expressiontool: Test timelimit in expressiontool is ignored
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpikopqnha --quiet tests/timelimit5.cwl tests/empty.json
Test [220/336] 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/tmprfycdvma --quiet tests/timelimit-wf.cwl tests/empty.json
[1;30mERROR[0m [31mTool definition failed validation:
tests/timelimit-wf.cwl:2:1: Object 'tests/timelimit-wf.cwl' is not valid because
tried 'Workflow' but
tests/timelimit-wf.cwl:18:1: the 'steps' field is not valid because
tried array of <WorkflowStep> but
tests/timelimit-wf.cwl:19:3: item is invalid because
tests/timelimit-wf.cwl:23:5: the 'run' field is not valid because
tests/timelimit-wf.cwl:29:7: the 'outputs' field is not valid because
tests/timelimit-wf.cwl:30:9: item is invalid because
tests/timelimit-wf.cwl:32:11: the 'outputBinding' field is not valid because
tried CommandOutputBinding but
tests/timelimit-wf.cwl:33:13: the 'outputEval' field is not valid because
tried Expression but
value 'time passed' does not contain an
expression in the form $() or ${}[0m
Test [221/336] 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/tmpyfm2q401 --quiet tests/timelimit2-wf.cwl tests/empty.json
Test [222/336] 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/tmpi2gn9z37 --quiet tests/timelimit3-wf.cwl tests/empty.json
Test [223/336] 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/tmpm56dbyjd --quiet tests/timelimit4-wf.cwl tests/empty.json
[1;30mERROR[0m [31mTool definition failed validation:
tests/timelimit4-wf.cwl:2:1: Object 'tests/timelimit4-wf.cwl' is not valid because
tried 'Workflow' but
tests/timelimit4-wf.cwl:21:1: the 'steps' field is not valid because
tried array of <WorkflowStep> but
tests/timelimit4-wf.cwl:22:3: item is invalid because
tests/timelimit4-wf.cwl:26:5: the 'run' field is not valid because
tests/timelimit4-wf.cwl:32:7: the 'outputs' field is not valid because
tests/timelimit4-wf.cwl:33:9: item is invalid because
tests/timelimit4-wf.cwl:35:11: the 'outputBinding' field is not valid because
tried CommandOutputBinding but
tests/timelimit4-wf.cwl:36:13: the 'outputEval' field is not valid because
tried Expression but
value 'time passed' does not contain an
expression in the form $() or ${}[0m
Test [224/336] networkaccess: Test networkaccess enabled
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpx_2xiqaa --quiet tests/networkaccess.cwl tests/empty.json
Test [225/336] networkaccess_disabled: Test networkaccess is disabled by default
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpeewfk31r --quiet tests/networkaccess2.cwl tests/empty.json
Test 225 failed: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpeewfk31r --quiet tests/networkaccess2.cwl tests/empty.json
Test networkaccess is disabled by default
Returned zero but it should be non-zero
Test [226/336] Test null and array input in InitialWorkDirRequirement
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpa1dag7y8 --quiet tests/stage-array.cwl tests/stage-array-job.json
Test [227/336] Test array of directories InitialWorkDirRequirement
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpao6o5pqu --quiet tests/stage-array-dirs.cwl tests/stage-array-dirs-job.yml
Test 227 failed: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpao6o5pqu --quiet tests/stage-array-dirs.cwl tests/stage-array-dirs-job.yml
Test array of directories InitialWorkDirRequirement
Compare failure expected: {
"output": [
{
"checksum": "sha1$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 [228/336] 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/tmp8fi6ydph --quiet tests/env-tool3.cwl tests/env-job3.yaml
Test [229/336] 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/tmp9kwtmb44 --quiet tests/env-tool4.cwl tests/env-job3.yaml
Test [230/336] 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/tmpn7jo9ofu --quiet tests/env-tool3.cwl tests/env-job4.yaml
Test [231/336] Test output of InitialWorkDir
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpvqohmeui --quiet tests/initialworkdir-glob-fullpath.cwl tests/initialworkdirrequirement-docker-out-job.json
Test [232/336] Test if full paths are allowed in glob
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmputry0tnk --quiet tests/initialworkdir-glob-fullpath.cwl tests/initialworkdirrequirement-docker-out-job.json
Test [233/336] Test fail trying to glob outside output directory
Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpu9c9g4xe --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 [234/336] 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/tmpi75yos_a --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/zr3pgl2y/symlink.txt'
in {
"output_file": {
"location": "file:///output/zr3pgl2y/symlink.txt",
"basename": "symlink.txt",
"nameroot": "symlink",
"nameext": ".txt",
"class": "Directory"
}
}[0m
Test [235/336] 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/tmphu8ifip4 --quiet tests/symlink-legal.cwl tests/empty.json
Test [236/336] inplace update has side effect on file content