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updated test submodule
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.travis.yml

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@@ -21,7 +21,7 @@ install:
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- conda config --add channels conda-forge
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- conda config --add channels bioconda
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- conda install -c bioconda -c conda-forge snakemake
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- conda create -q -n snakemake snakemake>=5.1.2 python=$TRAVIS_PYTHON_VERSION
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- conda create -q -n snakemake snakemake>=5.3.1 python=$TRAVIS_PYTHON_VERSION
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script:
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# run the workflow
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- snakemake --use-conda --directory .test -p

scripts/plot_species_plot.R

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@@ -123,10 +123,8 @@ df=categorizeCellsUsingKneeKnownNumCellsPaper(digitalExpressionFileO1,
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point.cex= 1,
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category = 'transcripts')
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dev.off()
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print(df)
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organism1 = subset(df, df$organism == organismOne)
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organism2 = subset(df, df$organism == organismTwo)
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print(organism1)
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write.table(organism1$tag, snakemake@output$barcodes_species[1], row.names=F, col.names=F, quote=F)
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write.table(organism2$tag, snakemake@output$barcodes_species[2], row.names=F, col.names=F, quote=F)

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