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celseq2
Commit 310ae513 authored by yy1533's avatar yy1533
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💪 keep annotation

parent 0a73460c
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Showing with 8 additions and 7 deletions
celseq2/workflow/celseq2_beta.snakemake
View file @ 310ae513
......@@ -102,7 +102,7 @@ SUBDIR_EXPR = 'expr'
SUBDIR_ST = 'ST'
SUBDIR_LOG = '.small_log'
SUBDIR_QSUB = 'qsub_log'
SUBDIR_ANNO = '.annotation'
SUBDIR_ANNO = 'annotation'
SUBDIR_REPORT = 'report'
SUBDIRS = [SUBDIR_INPUT,
......@@ -139,7 +139,8 @@ if RUN_CELSEQ2_TO_ST:
mkfolder(SUBDIR_QSUB)
shell('mv -f celseq2_job*.sh* {}'.format(SUBDIR_QSUB))
if not KEEP_INTERMEDIATE:
rmfolder(SUBDIR_FASTQ); rmfolder(SUBDIR_ANNO);
rmfolder(SUBDIR_FASTQ);
# rmfolder(SUBDIR_ANNO);
rmfolder(SUBDIR_ALIGN); rmfolder(SUBDIR_ALIGN_ITEM);
rmfolder(SUBDIR_LOG);
rmfolder(SUBDIR_UMI_CNT); rmfolder(SUBDIR_UMI_SET);
......@@ -157,7 +158,8 @@ else:
mkfolder(SUBDIR_QSUB)
shell('mv -f celseq2_job*.sh* {}'.format(SUBDIR_QSUB))
if not KEEP_INTERMEDIATE:
rmfolder(SUBDIR_FASTQ); rmfolder(SUBDIR_ANNO);
rmfolder(SUBDIR_FASTQ);
# rmfolder(SUBDIR_ANNO);
rmfolder(SUBDIR_ALIGN); rmfolder(SUBDIR_ALIGN_ITEM);
rmfolder(SUBDIR_LOG);
rmfolder(SUBDIR_UMI_CNT); rmfolder(SUBDIR_UMI_SET);
......@@ -238,8 +240,8 @@ if RUN_CELSEQ2_TO_ST:
rule combo_demultiplexing:
input: SAMPLE_TABLE_FPATH,
output:
fq = dynamic(join_path(DIR_PROJ, SUBDIR_FASTQ,
'{itemid}', '{bc}.fastq')),
fq = temp(dynamic(join_path(DIR_PROJ, SUBDIR_FASTQ,
'{itemid}', '{bc}.fastq'))),
message: 'Performing combo-demultiplexing'
params:
jobs = len(item_names),
......@@ -412,8 +414,7 @@ rule COOK_ANNOTATION:
output:
anno_pkl = temp(join_path(DIR_PROJ, SUBDIR_ANNO,
base_name(GFF) + '.pickle')),
anno_csv = temp(join_path(DIR_PROJ, SUBDIR_ANNO,
base_name(GFF) + '.csv')),
anno_csv = join_path(DIR_PROJ, SUBDIR_ANNO, base_name(GFF) + '.csv'),
flag = '_done_annotation',
params:
gene_type = GENE_BIOTYPE
......
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