Commit cfebaf2f authored by yy1533's avatar yy1533

💊 plotly graph on demultiplexing fastqs

parent f11f7835
......@@ -43,6 +43,10 @@ Refs:
- https://bitbucket.org/snakemake/snakemake/src/e11a57fe1f62f3f56c815d95d82871811dae81b3/snakemake/__init__.py?at=master&fileviewer=file-view-default#__init__.py-580:1127
'''
task_choices = ['all', 'TAG_FASTQ', 'ANNOTATION', 'ALIGNMENT',
'COUNT_MATRIX', 'QC_COUNT_MATRIX', 'CELSEQ2_TO_ST',
'REPORT']
def get_argument_parser():
desc = ('celseq2: A Python Package for Processing CEL-Seq2 RNA-Seq Data.')
......@@ -52,9 +56,9 @@ def get_argument_parser():
"target",
nargs="*",
default=None,
help="Targets to build. May be rules or files.",
choices=[None, 'all', 'TAG_FASTQ', 'ANNOTATION', 'ALIGNMENT',
'COUNT_MATRIX', 'QC_COUNT_MATRIX', 'CELSEQ2_TO_ST'])
help=('Targets to build. '
'May be rules or files. '
'Task choices: {}').format(', '.join(task_choices)))
parser.add_argument(
"--config-file",
metavar="FILE",
......
......@@ -679,10 +679,11 @@ rule report_combo_demultiplexing:
output:
html = join_path(DIR_PROJ, SUBDIR_REPORT, 'demultiplexing_fastq.html')
run:
# Prepare the stats files
# stats files [/path/item-1/d.csv, /path/item-2/d.csv]
stats_fpaths = glob.glob(join_path(DIR_PROJ, SUBDIR_REPORT,
'item-*', 'demultiplexing.csv'))
stats_fpaths_labels = [base_name(base_name(f)) for f in stats_fpaths]
# labels [item-1, item-2]
stats_fpaths_labels = [base_name(dir_name(f)) for f in stats_fpaths]
work = plotly_demultiplexing_stats(
fpaths=stats_fpaths,
saveto=output.html,
......
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