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yyoshiaki / VIRTUS2

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
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Warnings: may be incompatible #17

Closed patrick-douglas closed 1 year ago

patrick-douglas commented 1 year ago

Dear All, Every time I run both VIRTUS and VIRTUS2 I receive the following warnings:

WARNING Workflow checker warning:
../../../../../../home/me/VIRTUS2/bin/VIRTUS.SE.cwl:228:9: Source 'output' of type ["null", "File"]
                                                           may be incompatible
../../../../../../home/me/VIRTUS2/bin/VIRTUS.SE.cwl:184:9:   with sink 'fq' of type "File"
../../../../../../home/me/VIRTUS2/bin/VIRTUS.SE.cwl:159:9: Source 'mappingstats' of type ["null",
                                                           "File"] may be incompatible
../../../../../../home/me/VIRTUS2/bin/VIRTUS.SE.cwl:245:9:   with sink 'input_STARLog' of type
                                                             "File"
../../../../../../home/me/VIRTUS2/bin/VIRTUS.SE.cwl:37:5:  Source 'filename_output' of type
                                                           ["null", "string"] may be incompatible
../../../../../../home/me/VIRTUS2/bin/VIRTUS.SE.cwl:251:9:   with sink 'filename_output' of type
                                                             "string"
../../../../../../home/me/VIRTUS2/bin/VIRTUS.SE.cwl:213:9: Source 'output' of type ["null", "File"]
                                                           may be incompatible
../../../../../../home/me/VIRTUS2/bin/VIRTUS.SE.cwl:235:9:   with sink 'input' of type "File"

Is there any way to fix it?

yyoshiaki commented 1 year ago

These are just warnings and ignorable. I may fix them in the future. Thank you for your report!

patrick-douglas commented 1 year ago

Hi, thank you for your reply. How can I run createindex using a local custom local virus database?

All best Patrick.

yyoshiaki commented 1 year ago

Hi, I made createref_localref.cwl in v2.0.2 (beta version). Please use https://github.com/yyoshiaki/VIRTUS2/blob/v2.0.2/workflow/createindex_localref.cwl and refer to the example input yaml, https://github.com/yyoshiaki/VIRTUS2/blob/v2.0.2/workflow/createindex_localref.job.yaml . Note that in the cwl, users also need to prepare the fasta file for the human genome.