pepr-hal-data / softcite /BioFlowInsightfacilitatingreuseofNextflowworkflowswithstructurereconstructionandvisualization.software.json
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"offsetEnd": 44}, "context": "In this article we introduce BioFlow-Insight , a tool to enhance reuse that inspects the code of Nextflow workflows and provides their structure.", "mentionContextAttributes": {"used": {"value": false, "score": 3.2901763916015625e-05}, "created": {"value": true, "score": 0.9999303817749023}, "shared": {"value": false, "score": 4.76837158203125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999874830245972}, "created": {"value": true, "score": 0.9999303817749023}, "shared": {"value": false, "score": 0.0006196498870849609}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "BioFlow", "normalizedForm": "BioFlow", "offsetStart": 38, "offsetEnd": 45}, "context": "Description of the errors detected by BioFlow-Insight, with the number of workflows that produce the error within the corpus of 677 open public w orkflo ws Errors due to BioFlow-Insight's limited Scope Error description Number of workflows 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"mentionContextAttributes": {"used": {"value": false, "score": 0.011714041233062744}, "created": {"value": false, "score": 0.00014138221740722656}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9998742341995239}, "created": {"value": true, "score": 0.9999303817749023}, "shared": {"value": false, "score": 0.33033502101898193}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Nextflow", "normalizedForm": "Nextflow", "offsetStart": 39, "offsetEnd": 47}, "context": "BioFlow-Insight analyses the code of a Nextflow workflow without executing it.", "mentionContextAttributes": {"used": {"value": false, "score": 0.00017756223678588867}, "created": {"value": false, "score": 3.814697265625e-06}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9998742341995239}, "created": {"value": true, "score": 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were due to confirmed code errors or ambiguities in the code (e.g., identically named processes and channels).", "mentionContextAttributes": {"used": {"value": true, "score": 0.9998317956924438}, "created": {"value": false, "score": 2.658367156982422e-05}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999337196350098}, "created": {"value": true, "score": 0.9999303817749023}, "shared": {"value": true, "score": 0.9957791566848755}}}, {"type": "software", "software-type": "implicit", "software-name": {"rawForm": "scripts", "normalizedForm": "scripts", "offsetStart": 40, "offsetEnd": 47}, "context": "Bioinformatics analyses conducted using scripts (e.g., bash or perl) are often challenging to share and execute on different computing environments.", "mentionContextAttributes": {"used": {"value": false, "score": 0.00019508600234985352}, "created": {"value": false, "score": 8.034706115722656e-05}, "shared": 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potential coding errors.", "mentionContextAttributes": {"used": {"value": false, "score": 2.9325485229492188e-05}, "created": {"value": false, "score": 0.0020037293434143066}, "shared": {"value": false, "score": 2.86102294921875e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9998742341995239}, "created": {"value": true, "score": 0.9999303817749023}, "shared": {"value": false, "score": 0.33033502101898193}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "BioFlow", "normalizedForm": "BioFlow", "offsetStart": 41, "offsetEnd": 48}, "context": "Finally, we hope to ultimately integrate BioFlow-Insight with platforms such as WorkflowHub ( 13 ) to facilitate the upload of workflows onto the platform.", "mentionContextAttributes": {"used": {"value": false, "score": 0.00024181604385375977}, "created": {"value": true, "score": 0.9173341393470764}, "shared": {"value": false, "score": 0.0003764629364013672}}, "documentContextAttributes": 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"software-name": {"rawForm": "Insight", "normalizedForm": "Insight", "offsetStart": 42, "offsetEnd": 49}, "context": "In the second section, we present BioFlow-Insight 's outputs, a use case, as well as an analysis on a workflow corpus.", "mentionContextAttributes": {"used": {"value": false, "score": 0.012562870979309082}, "created": {"value": true, "score": 0.999771773815155}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999874830245972}, "created": {"value": true, "score": 0.9999303817749023}, "shared": {"value": false, "score": 0.0006196498870849609}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Insight", "normalizedForm": "Insight", "offsetStart": 42, "offsetEnd": 49}, "context": "Thanks to the graphs generated by BioFlow-Insight , understanding the individual steps of a workflow and how they are connected becomes significantly easier.", "mentionContextAttributes": {"used": {"value": false, "score": 0.00014102458953857422}, "created": {"value": false, "score": 0.040016770362854004}, "shared": {"value": false, "score": 5.960464477539062e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999874830245972}, "created": {"value": true, "score": 0.9999303817749023}, "shared": {"value": false, "score": 0.0006196498870849609}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Insight", "normalizedForm": "Insight", "offsetStart": 43, "offsetEnd": 50}, "context": "A final point to mention regarding BioFlow-Insight 's usefulness is that it allows developers to compare the graphs generated by BioFlow-Insight , which are derived from the workflow's implementation, with the workflow structure drawings in the documentation (often designed during the predevelopment phase).", "mentionContextAttributes": {"used": {"value": false, "score": 0.00016510486602783203}, "created": {"value": false, "score": 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"software-type": "software", "software-name": {"rawForm": "Insight", "normalizedForm": "Insight", "offsetStart": 46, "offsetEnd": 53}, "context": "Description of the errors detected by BioFlow-Insight, with the number of workflows that produce the error within the corpus of 677 open public w orkflo ws Errors due to BioFlow-Insight's limited Scope Error description Number of workflows Unknown element used in a pipe operator 1 Ternary conditional operator used with a tuple 2 Tuple associated with a call 5 Errors or ambiguities detected in the workflow's code Error description Number of workflows", "mentionContextAttributes": {"used": {"value": true, "score": 0.9990135431289673}, "created": {"value": false, "score": 1.5497207641601562e-06}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999874830245972}, "created": {"value": true, "score": 0.9999303817749023}, "shared": {"value": false, "score": 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"mentionContextAttributes": {"used": {"value": false, "score": 0.0019192695617675781}, "created": {"value": false, "score": 0.0002440810203552246}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999337196350098}, "created": {"value": true, "score": 0.9999310970306396}, "shared": {"value": true, "score": 0.9957791566848755}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "BioFlow-Insight", "normalizedForm": "BioFlow-Insight", "offsetStart": 49, "offsetEnd": 64}, "version": {"rawForm": "3", "normalizedForm": "3"}, "url": {"rawForm": "https:// doi.org/ 10.6084/ m9. figshare", "normalizedForm": "https:// doi.org/ 10.6084/ m9. figshare"}, "context": "Table describes the various errors detected by BioFlow-Insight along with the number of workflows that produce each error.", "mentionContextAttributes": {"used": {"value": true, "score": 0.8916890025138855}, "created": {"value": 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"documentContextAttributes": {"used": {"value": true, "score": 0.9999337196350098}, "created": {"value": true, "score": 0.9999303817749023}, "shared": {"value": true, "score": 0.9957791566848755}}}, {"type": "software", "software-type": "implicit", "software-name": {"rawForm": "code", "normalizedForm": "code", "offsetStart": 209, "offsetEnd": 213}, "context": "By doing so, BioFlow-Insight can detect programming errors that affect the structure / syntax of the workflow, such as a wrong number of parameters given in a call, a missing file, or a missing element in the code (see Table for the list of detected errors).", "mentionContextAttributes": {"used": {"value": false, "score": 6.914138793945312e-05}, "created": {"value": false, "score": 0.001694321632385254}, "shared": {"value": false, "score": 1.1920928955078125e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999337196350098}, "created": {"value": true, "score": 0.9999303817749023}, "shared": {"value": true, 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"offsetStart": 411, "offsetEnd": 415}, "context": "Description of the errors detected by BioFlow-Insight, with the number of workflows that produce the error within the corpus of 677 open public w orkflo ws Errors due to BioFlow-Insight's limited Scope Error description Number of workflows Unknown element used in a pipe operator 1 Ternary conditional operator used with a tuple 2 Tuple associated with a call 5 Errors or ambiguities detected in the workflow's code Error description Number of workflows", "mentionContextAttributes": {"used": {"value": true, "score": 0.9990135431289673}, "created": {"value": false, "score": 1.5497207641601562e-06}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999337196350098}, "created": {"value": true, "score": 0.9999303817749023}, "shared": {"value": true, "score": 0.9957791566848755}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "code", "normalizedForm": "code", "offsetStart": 494, "offsetEnd": 498}, "context": "Incorrect number of parameters given for a process or a subworkflow call 16 Channel trying to be created with a name already given to an existing element 27 Multiple channels are given by an emit even though only expecting one 1 Tried to access an emit even though the element its emitting has not been called 16 Tried to include a file which does not exist 14 An include was present in a main or subworkflow 1 In a pipe operator, the first element called does not exist 11 Syntax error in the code (e.g., not the same number of opening and closing parentheses) 34 Element (process or subworkflow) is expected to be defined in a file but is not 8 A subworkflow either emits nothing or too many values for use in an operation 20 A subworkflow or process was defined badly (e.g., multiple input sections, multiple main sections...) 10", "mentionContextAttributes": {"used": {"value": true, "score": 0.9985881447792053}, 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