Commit d85c2668 authored by yy1533's avatar yy1533
Browse files

💪 flexibility to choose gene_name or gene_id. See issue #2

parent 44c7d9f0
......@@ -12,7 +12,11 @@ BOWTIE2_INDEX_PREFIX: '/absolute/path/to/bowtie2_index'
BOWTIE2: '/absolute/path/to/bowtie2'
## Annotations ##
# Path to GTF/GFF file
GFF: '/absolute/path/to/wonderful.gtf.gz'
# Refer: http://htseq.readthedocs.io/en/master/count.html
FEATURE_ID: 'gene_name'
FEATURE_CONTENT: 'exon'
## Demultiplexing ##
FASTQ_QUAL_MIN_OF_BC: 10
......
......@@ -41,6 +41,8 @@ BOWTIE2 = config.get('BOWTIE2', None) # '/local/apps/bowtie2/2.3.1/bowtie2'
## Annotations ##
# '/ifs/data/yanailab/refs/danio_rerio/danRer10_87/gtf/Danio_rerio.GRCz10.87.gtf.gz'
GFF = config.get('GFF', None)
FEATURE_ID = config.get('FEATURE_ID', 'gene_name')
FEATURE_CONTENT = config.get('FEATURE_CONTENT', 'exon')
## Demultiplexing ##
FASTQ_QUAL_MIN_OF_BC = config.get('FASTQ_QUAL_MIN_OF_BC', None) # 10
......@@ -237,8 +239,8 @@ rule cook_annotation:
flag = touch('_done_annotation'),
message: 'Cooking Annotation'
run:
_ = cook_anno_model(GFF, feature_atrr='gene_id',
feature_type='exon',
_ = cook_anno_model(GFF, feature_atrr=FEATURE_ID,
feature_type=FEATURE_CONTENT,
stranded=True,
dumpto=output.anno,
verbose=verbose)
......
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