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yuch7 / cwlexec

A new open source tool to run CWL workflows on LSF
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ScatterFeature does not accept list of files as input: Java ClassCastException thrown #43

Closed mscheremetjew closed 5 years ago

mscheremetjew commented 5 years ago

Not sure if I am doing anything wrong, but it works that way with the CWL tool description reference implementation. Any advice would be appreciated.

Here is the workflow and a YAML job description: issue_43.zip

command: $ unzip issue_43.zip $ cd issue_43 $ cwlexec -X -p --workdir /home/user/output/ cmsearch-multimodel-wf.cwl jobs/cmsearch-multimodel-wf.test.job.yaml

cwlexec stops and reports the following:

16:13:44.227 default [main] DEBUG c.i.s.c.e.util.command.CommandUtil - The command input argument: 1000 for step cmsearch
16:13:44.227 default [main] DEBUG c.i.s.c.e.util.command.CommandUtil - The command input argument: 1000 for step cmsearch
16:13:44.227 default [main] DEBUG c.i.s.c.e.util.command.CommandUtil - The input (id=covariance_model_database, type=File, value=File:/home/user/maxim/output/cwlexec/7fd4f443-eab1-4fd5-b767-7a68add47c5d/cmsearch/tRNA5.c.cm) of step cmsearch
16:13:44.227 default [main] DEBUG c.i.s.c.e.util.command.CommandUtil - The command input argument: /home/user/maxim/output/cwlexec/7fd4f443-eab1-4fd5-b767-7a68add47c5d/cmsearch/tRNA5.c.cm for step cmsearch
16:13:44.227 default [main] DEBUG c.i.s.c.e.util.command.CommandUtil - The input (id=query_sequences, type=File, value=File:/home/user/maxim/output/cwlexec/7fd4f443-eab1-4fd5-b767-7a68add47c5d/cmsearch/mrum-genome.fa) of step cmsearch
16:13:44.227 default [main] DEBUG c.i.s.c.e.util.command.CommandUtil - The command input argument: /home/user/maxim/output/cwlexec/7fd4f443-eab1-4fd5-b767-7a68add47c5d/cmsearch/mrum-genome.fa for step cmsearch
16:13:44.227 default [main] DEBUG c.i.s.c.e.util.command.CommandUtil - Has Shell Command, build commands as:
[cmsearch, --tblout, mrum-genome.fa.cmsearch_matches.tbl, -o, mrum-genome.fa.cmsearch.out, --cpu, 1, --noali, --hmmonly, -Z, 1000, /home/user/maxim/output/cwlexec/7fd4f443-eab1-4fd5-b767-7a68add47c5d/cmsearch/tRNA5.c.cm, /home/user/maxim/output/cwlexec/7fd4f443-eab1-4fd5-b767-7a68add47c5d/cmsearch/mrum-genome.fa]
java.util.ArrayList cannot be cast to com.ibm.spectrumcomputing.cwl.model.process.parameter.type.file.CWLFile
16:13:44.235 default [Thread-3] DEBUG c.i.s.cwl.exec.CWLExec - Stop cwlexec...
16:13:44.236 default [Thread-3] DEBUG c.i.s.cwl.exec.CWLExec - cwlexec has been stopped
skeeey commented 5 years ago

@mscheremetjew This should be a cwlexec bug, we are in the Spring Festival vacation, after we come back from the vacation we will fix it

adamsla commented 5 years ago

Our development team, have some amazing national holiday schedules. For me, it's nice to see that where they are, their government respects their peoples right and ability to take this time to share with family and friends.

qiangjia commented 5 years ago

@mscheremetjew Please rebuild the package and try again, and please modify line 17 of concatenate.cwl, change type: File -> type: File[] before start running.

mscheremetjew commented 5 years ago

@skeeey @qiangjia Tested successfully. Many Thanks for the fix.