Commit 7a75426a authored by khalid's avatar khalid
Browse files

Change htseq-count name

parent b66322cb
rule <step_name>__htseq-count:
rule <step_name>__htseq_count:
input:
**<step_name>__htseq-count_inputs()
**<step_name>__htseq_count_inputs()
output:
stats = config["results_dir"]+'/' + config["<step_name>__htseq-count_output_dir"] + '/{sample}.txt',
stats = config["results_dir"]+'/' + config["<step_name>__htseq_count_output_dir"] + '/{sample}.txt',
log:
config["results_dir"]+'/logs/' + config["<step_name>__htseq-count_output_dir"] + '/{sample}_htseq-count_log.txt'
config["results_dir"]+'/logs/' + config["<step_name>__htseq_count_output_dir"] + '/{sample}_htseq_count_log.txt'
params:
command = config["<step_name>__htseq-count_command"],
htseq_count_minaqual = config["htseq-count_minaqual"],
command = config["<step_name>__htseq_count_command"],
htseq_count_minaqual = config["htseq_count_minaqual"],
htseq_stranded = config["htseq_stranded"],
output_dir = config["results_dir"]+'/'+config["<step_name>__htseq-count_output_dir"]
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}"
"{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}"
{
id: htseq-count,
name: Htseq-count,
id: htseq_count,
name: Htseq_count,
article: doi:10.1093/bioinformatics/btu638,
website: "https://htseq.readthedocs.io",
git: "https://github.com/htseq/htseq",
description: "A tool to quantify gene expression in RNA-Seq and similar experiments.",
version: "release_0.13.5",
documentation: "https://htseq.readthedocs.io",
multiqc: "htseq-count",
multiqc: "htseq_count",
commands:
[
{
name: htseq-count,
name: htseq_count,
command: htseq-count,
category: "quantification",
output_dir: htseq-count,
output_dir: htseq_count,
inputs: [
{ name: bam, type: "bams" },
{ name: gff_file, type: "gff3"}
],
outputs:
[
{ name: stats, type: "txt", file: "{sample}_htseq-count.txt", description: "a table with counts for each feature" }
{ name: stats, type: "txt", file: "{sample}_htseq_count.txt", description: "a table with counts for each feature" }
],
options:
[
......
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