def pipeline():
return get_pipeline(__file__).set_starts(Download).set_data([
"https://www.ncbi.nlm.nih.gov/geo/download/"
"?acc=GSE179367"
"&format=file"
"&file=GSE179367%5Fgene%5Fcount%2Ereal%2Etxt%2Egz",
])
def pipeline():
return get_pipeline(__file__).set_starts(
BedConsensus,
BedConsensus1,
).set_data([[
Path(__file__).parent / "data" / "in1.bed",
Path(__file__).parent / "data" / "in2.bed",
Path(__file__).parent / "data" / "in3.bed",
]])
def pipeline():
return get_pipeline(__file__).set_starts(Str2File).set_data([(
("Meta\tId\tsymbol\n"
"a\t1255_g_at\t1\n"
"b\t1294_at\t2\n"
"c\t1316_at\t3\n"
"d\tnonexist\t4\n"
"e\t1320_at\t5\n"),
"data.txt",
)])
def pipeline():
return (
get_pipeline(__file__)
.set_start(DownloadData)
.set_data(
[
"https://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123813/"
"suppl/GSE123813_bcc_tcell_metadata.txt.gz",
"https://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123813/"
"suppl/GSE123813_bcc_scRNA_counts.txt.gz",
]
)
)
def pipeline():
return get_pipeline(__file__).set_starts(Download, Str2File).set_data(
[
"https://www.ncbi.nlm.nih.gov/geo/download/"
"?acc=GSE179367"
"&format=file"
"&file=GSE179367%5Fgene%5Fcount%2Ereal%2Etxt%2Egz",
"https://www.genepattern.org/tutorial/linkedFiles/"
"export_gnf.GENE_SYMBOL.gmt",
],
[(
(
"Sample\tGroup\n"
"shMMP9_1\tMMP9\n"
"shMMP9_2\tMMP9\n"
"shMMP9_3\tMMP9\n"
"shControl_1\tCTRL\n"
"shControl_2\tCTRL\n"
"shControl_3\tCTRL\n"
),
"samples.txt"
)]
)
def pipeline():
return get_pipeline(__file__).set_starts(PrepareSeurat)
def pipeline():
return get_pipeline(__file__).set_starts(PrepareImmdata)
def pipeline():
return get_pipeline(__file__).set_starts(Bed2Vcf).set_data(
[Path(__file__).parent / "data" / "in.bed"]
)
def pipeline():
return (get_pipeline(__file__).set_start(DownloadList).set_data(
[Path(__file__).parent / "data" / "vcfs.txt"]))
