Commit 0b6405af authored by khalid's avatar khalid
Browse files

debug raw_gff3

parent e7dd4dff
......@@ -11,7 +11,7 @@ rule <step_name>__hisat2_index:
config["<step_name>__hisat2_index_threads"]
params:
command = config["<step_name>__hisat2_index_command"],
output_prefix = config["<step_name>__hisat2_index_output_dir"]+"/index"
output_prefix = config["results_dir"]+"/"+config["<step_name>__hisat2_index_output_dir"]+"/index"
shell:
"{params.command} "
"{input.genome_fasta} "
......
......@@ -9,6 +9,7 @@ rule <step_name>__htseq_count:
command = config["<step_name>__htseq_count_command"],
htseq_count_minaqual = config["<step_name>__htseq_count_minaqual"],
htseq_stranded = config["<step_name>__htseq_stranded"],
htseq_orientation = config["<step_name>__htseq_orientation"],
output_dir = config["results_dir"]+'/'+config["<step_name>__htseq_count_output_dir"]
shell:
"{params.command} -f bam -a {params.htseq_count_minaqual} -s {params.htseq_stranded} -r {params.htseq_orientation} {input.bam} {input.gff_file} 2> {log} > {output.stats}"
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