Fastq and bamindex creation to workdir if necessary

NBISweden / wgs-structvar

Whole Genome Sequenceing Structural Variation Pipelines

GNU General Public License v3.0

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Closed glormph closed 7 years ago

glormph commented 7 years ago

Addresses issues #82, #83 This PR:

Removed fastq/indexed bamfile from input to fastqcreator/bam indexer so that when they are run, the files end up in workdir and not current launch dir
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