Zuzu/testcommand at main · BenjaminATaylor/Zuzu · GitHub

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nextflow run main.nf \
   #--samplesheet "input/test3/samplesheet_phenotype.csv" \
   #--countsframe "input/test3/GSE91061_BMS038109Sample.hg19KnownGene.raw.tsv" \
   #--reflevel "Pre-treatment" \
    --samplesheet "input/test2/samplesheet_phenotype.csv" \
    --countsframe "input/test2/salmon.merged.gene_counts.tsv" \
    --reflevel "nurse" \
    --outdir "output" \
    --nperms 20 \
    --truecutoff 0.00001 \
    --synthstep true \
    --synthdeg_pct 0.1 \
    --mlstep false \
    --pareml true \
    -w work \
    -resume

nextflow run main.nf \
    --samplesheet "input/test5/samplesheet.csv" \
    --countsframe "input/test5/salmon.merged.gene_counts.tsv" \
    --reflevel "nurse" \
    --outdir "output" \
    --nperms 3 \
    --truecutoff 0.00001 \
    --synthstep true \
    --synthdeg_pct 0.1 \
    --mlstep true \
    --pareml true \
    --stepsize 10 \
    -w work \
    -resume