Zuzu/testcommand at main · BenjaminATaylor/Zuzu · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
#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 3 \
#    --truecutoff 0.00001 \
#    --synthstep true \
#    --synthdeg_pct 0.1 \
#    --mlstep false \
#    --pareml true \
#    -w work \
#    -resume

nextflow run main.nf \
    -profile local \
    --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 false \
    --stepsize 10 \
    -w work \
    -resume