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--outdir #25

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portah opened this issue Nov 26, 2015 · 1 comment
Closed

--outdir #25

portah opened this issue Nov 26, 2015 · 1 comment

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@portah
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portah commented Nov 26, 2015

I did not find a way to put file into ./test-files and do not have a cwltool error. I can either output it into the dir but have workflow error or have it in current dir and no errors.

When I run command cwltool --outdir ./test-files/ ./samtools-index.cwl ./jobs/samtools-index-job.json file .bai created in ./test-files but I have an error from cwltool

Error while running job: Did not find output file with glob pattern: '[u'SRR1031972.Aligned.sortedByCoord.out.bam.bai']'
[job 4463785808] completed permanentFail
Final process status is permanentFail
Workflow error:
  Process status is ['permanentFail']

Or I can run cwltool ./samtools-index.cwl ./jobs/samtools-index-job.json but then file in current directory :(
@portah
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portah commented Nov 26, 2015

Sorry found a way
cwltool --basedir ./ --outdir ./test-files ./samtools-index.cwl ./jobs/samtools-index-job.json

@portah portah closed this as completed Nov 26, 2015
tetron pushed a commit that referenced this issue Jun 8, 2016
Squashed 'cwltool/schemas/' changes from f027dbb..d03b190
b9b65c0 
d03b190 Introducing refScope and typeDSL into CWL schema
5e1e438 Merge commit '851b3c1302aa5b5d8a80f74c5732a617f62acefe' into scoped-ref-and-typedsl
851b3c1 Split minimal base types used in CWL into metaschema_base.yml
510a01f Merge commit '8823aaa11432aa042b3e307891e71ee13e11bfd7' into scoped-ref-and-typedsl
8823aaa Adjust ref scopes
3431e18 Use scopedRef and typeDSL in metaschema
1e6dab6 Using typeDSL in metaschema.
3055f70 Update bootstrap context.
31db28e Merge branch 'master' into type_dsl.  Add test for typeDSL.
116d9e4 Merge branch 'resolve_all_refactor'
8072bf5 "type" DSL wip
33ef215 Refactor resolve_all into smaller methods.
ad8a111 Merge pull request #28 from common-workflow-language/scoped_ref
5aadf27 fix types
4ef52be Improve documentation.  Add feature of skipping some inner scopes.
c6d4a7b Reworking refScope to be fixed instead of search based.
ae0ef4e Remove explicit calls to validate_links since it is folded into resolve_all().
2fa6bfb update types
e5d4730 New test for scoped ref that better reflects actual desired behavior.
efbc9c4 Add scopedRef to metaschema.  Tweak test.
9fcd67d Fold link validation into resolve_all() and resolve scoped identifiers.
f36f52f Merge pull request #219 from denis-yuen/patch-1
da10eec always be updating (mypy-lang)
e1e17ea upgrade Jenkins setuptools
563e5ef fix jenkins build
11b45b5 Merge pull request #224 from common-workflow-language/jenkins-link
b4d790d Backport fixes to draft-3
1ea9a5c add jenkins link
180a21e Corrections and test data
f0ac285 Merge branch 'master' of github.com:common-workflow-language/schema_salad
84738f1 better RDF schema error handling (#26)
3b8dc09 mypy 0.4 is out (#25)
5316da0 Add missing files for site generation.
31fbb76 Fix site generation workflows to specify draft-3
cff09a0 Add link to latest User Guide on front page
53b2ad7 Merge pull request #200 from common-workflow-language/draft-4
089fbd7 start documenting the draft-4 changes
8c5bda0 Fix mapSubject fields when $import or $include is provided.
5b969ca fix diff-cover
d798a7e split out mypy
f43fa45 Fix tests
2d0398e Bump version.
aeab7c3 Merge branch 'master' of github.com:common-workflow-language/schema_salad
e381f64 Return metaschema loader from load_schema.  Don't crash expanding identifier fields when value is not a string.
15dae9f enhance CI
fd2fcb3 more type checking (#21)
c51c723 enable rdfa schema format (#22)
ff192e8 turn off py3 support for now (#19)
0c5dba5 measure code coverage (#12)
2514a23 switch to ruamel.yaml, use C loader if available, only load safely (#20)

git-subtree-dir: cwltool/schemas
git-subtree-split: d03b190
mr-c added a commit that referenced this issue Jul 6, 2016
@mr-c
mypy 0.4 is out (#25)
3b8dc09
mr-c pushed a commit that referenced this issue Jul 6, 2016
Squashed 'draft-4/salad/' changes from 9c8c36f..c509a07
6266928 
c509a07 Merge pull request #34 from common-workflow-language/unscoped_ids
f857e9d type fixups
0407370 Allow idmaps for record fields.
5d9a08e Use makerdf for --print-rdf
ce00252 Add test for non-scoped identifiers.
ef27301 restore a dropped cast
6ac559e version bump
2cfde6b Merge pull request #32 from common-workflow-language/type_dsl
b8edddc re-enable test_avro_regression
bedb736 Merge branch 'type_dsl' of github.com:common-workflow-language/schema_salad into type_dsl
e93b038 Add missing file
9ca6cc9 remove more str types, possible fix for edam failed test
d65fb83 more unicode
4350b30 type clarification
96f08e8 Merge remote-tracking branch 'origin/master' into type_dsl
57f7e83 borrow the updated re.pyi from typeshed
c03eb1e type fixes
6e71f35 Merge remote-tracking branch 'origin/master' into type_dsl
e554b2b Merge pull request #33 from common-workflow-language/fix-resolve_all_refactor
ad34521 fix bug introduced by refactor
5393edc fixes types, removes a few more Anys
e298bdc Detect when an abstract class is used but doesn't have a concrete subtype.
851b3c1 Split minimal base types used in CWL into metaschema_base.yml
8823aaa Adjust ref scopes
3431e18 Use scopedRef and typeDSL in metaschema
1e6dab6 Using typeDSL in metaschema.
3055f70 Update bootstrap context.
31db28e Merge branch 'master' into type_dsl.  Add test for typeDSL.
116d9e4 Merge branch 'resolve_all_refactor'
8072bf5 "type" DSL wip
33ef215 Refactor resolve_all into smaller methods.
ad8a111 Merge pull request #28 from common-workflow-language/scoped_ref
5aadf27 fix types
4ef52be Improve documentation.  Add feature of skipping some inner scopes.
c6d4a7b Reworking refScope to be fixed instead of search based.
ae0ef4e Remove explicit calls to validate_links since it is folded into resolve_all().
2fa6bfb update types
e5d4730 New test for scoped ref that better reflects actual desired behavior.
efbc9c4 Add scopedRef to metaschema.  Tweak test.
9fcd67d Fold link validation into resolve_all() and resolve scoped identifiers.
da10eec always be updating (mypy-lang)
e1e17ea upgrade Jenkins setuptools
563e5ef fix jenkins build
f0ac285 Merge branch 'master' of github.com:common-workflow-language/schema_salad
84738f1 better RDF schema error handling (#26)
3b8dc09 mypy 0.4 is out (#25)
8c5bda0 Fix mapSubject fields when $import or $include is provided.
5b969ca fix diff-cover
d798a7e split out mypy
f43fa45 Fix tests
2d0398e Bump version.
aeab7c3 Merge branch 'master' of github.com:common-workflow-language/schema_salad
e381f64 Return metaschema loader from load_schema.  Don't crash expanding identifier fields when value is not a string.
15dae9f enhance CI
fd2fcb3 more type checking (#21)
c51c723 enable rdfa schema format (#22)
ff192e8 turn off py3 support for now (#19)
0c5dba5 measure code coverage (#12)
2514a23 switch to ruamel.yaml, use C loader if available, only load safely (#20)
37c129d Merge branch 'master' of github.com:common-workflow-language/schema_salad
0b09a19 Makedoc detects any ``` for toggling looking for # for section headings.
d361b6c Bump version #
2da084e Add mapSubject and mapPredicate to metaschema.
2b00752 Turn idMap into mapSubject and mapPredicate.
af7a419 Support id maps in preprocessing.
984ab9c Fix makedoc section header bug.
cc0f52b Add margin to <pre> sections in generated documentation.

git-subtree-dir: draft-4/salad
git-subtree-split: c509a07
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@portah