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gem-pasteur / Integron_Finder
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LAST BUILD BRANCH: issue_69
DEFAULT BRANCH: master
Repo Added 04 Jan 2017 03:03PM UTC
Files 32
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bneron
:bug: fix problem with parallel_integron_finder with --gembase

when use --gembase the genbase folder is compute from the replicon path
but with the parallel version the input files are generated by plit and
located in the work treefile
so it's not so obvious to retrieve the gemabse directory
further more after the split step the basenae it self are modified
 for draft we have file nae as contig
 for complete we have _chunk_id postfix file

so I add new option --gemabse-path to explicitely passed the gembase
root directory
only this option is enable for workflow
the both are available for sequential version.

1516 of 1601 relevant lines covered (94.69%)

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2.84 HITS PER LINE
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Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
271 dev :bug: fix problem with parallel_integron_finder with --gembase when use --gembase the genbase folder is compute from the replicon path but with the parallel version the input files are generated by plit and located in the work treefile so it's no... push 06 Mar 2019 04:13PM UTC bneron travis-ci pending completion  
258 dev :pencil2: add precision about virtualenv creation push 18 Feb 2019 12:57PM UTC bneron travis-ci pending completion  
257 dev :bug: fix maock to call (need more argument) push 18 Feb 2019 12:40PM UTC bneron travis-ci pending completion  
246 dev use the latest singularity image push 14 Dec 2018 10:44AM UTC bneron travis-ci pending completion  
243 dev :pencil2: add api doc for 'prot_db' and 'results' modules push 14 Dec 2018 09:34AM UTC bneron travis-ci pending completion  
241 dev :bug: when an erro occured in one task all tasks are stopped change the default strategy to look for integrons for all sequences where it is possible and not stopping the whole workflow at the first error errorStrategy = 'ignore' push 08 Nov 2018 03:40PM UTC bneron travis-ci pending completion  
237 dev Merge branch 'feat_empty_file' push 23 Oct 2018 03:15PM UTC bneron travis-ci pending completion  
230 dev :pnecil2: add doc about new pattern as input push 02 Oct 2018 02:06PM UTC bneron travis-ci pending completion  
227 dev :art: simplify channels between split and merge process it's need to have only one chanel to transmit file_id, nb of chunks and file from split to integron_finder push 01 Oct 2018 03:46PM UTC bneron travis-ci pending completion  
224 dev :fix: topology if replicon file contain only one seq the test on the number of sequence in replicon file failed push 28 Sep 2018 07:38PM UTC bneron travis-ci pending completion  
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