In according to the current version of the Fonda fusionCatcher tool template contains the following line:
mv {fusionCatcherFields.fusionCatcherOutdir}/fusionCatcher.fusion_candidates.final.abridged {fusionCatcherFields.fusionCatcherOutdir}.
This is not only pointless but the specified fusionCatcher.fusion_candidates.final.abridge file is not the result of this tool, and it was not found accordingly. Possible tool outputs are listed here: https://github.com/ndaniel/fusioncatcher/blob/master/doc/manual.md#62---output-data-output-data
Approach
Suppose, that the correct option is:
mv {fusionCatcherFields.fusionCatcherOutdir}/final-list_candidate_fusion_genes.txt {fusionCatcherFields.fusionCatcherResult}
Background
In according to the current version of the Fonda fusionCatcher tool template contains the following line:
mv {fusionCatcherFields.fusionCatcherOutdir}/fusionCatcher.fusion_candidates.final.abridged {fusionCatcherFields.fusionCatcherOutdir}. This is not only pointless but the specifiedfusionCatcher.fusion_candidates.final.abridgefile is not the result of this tool, and it was not found accordingly. Possible tool outputs are listed here:https://github.com/ndaniel/fusioncatcher/blob/master/doc/manual.md#62---output-data-output-data
Approach
Suppose, that the correct option is:
mv {fusionCatcherFields.fusionCatcherOutdir}/final-list_candidate_fusion_genes.txt {fusionCatcherFields.fusionCatcherResult}