Commit 506f0f69 authored by khalid's avatar khalid
Browse files

Add htseq-count

parent 761fc5a5
rule <step_name>__htseq-count:
input:
**<step_name>__htseq-count_inputs()
output:
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'
params:
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"]
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}"
{
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",
commands:
[
{
name: htseq-count,
command: htseq-count,
category: "quantification",
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" }
],
options:
[
{
name: htseq-count_minaqual,
prefix: -a,
type: numeric,
value: 10,
min: 1,
max: 80,
step: 1,
label: "skip all reads with alignment quality lower than the given minimum value",
},
{
name: htseq_stranded,
type: radio,
choices:
[
Not stranded: "no",
Stranded: "yes",
Reverse Stranded: "reverse",
],
value: "no",
label: "whether the data is from a strand-specific assay.",
},
{
name: htseq_orientation,
type: radio,
choices:
[
Position: "position",
Name: "name"
],
value: "position",
label: "the way that alignment have been sorted (either by read name or by alignment position).",
},
],
},
],
install: {
htseq: [
"pip3 install "HTSeq==0.13.5"
]
},
citations: {
htseq: [
"Simon Anders, Paul Theodor Pyl, Wolfgang Huber. HTSeq - A Python framework to work with high-throughput sequencing data Bioinformatics (2014)."
]
}
}
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