Commit c2680e81 authored by khalid's avatar khalid
Browse files

debug htseq-count

parent 3bab8250
......@@ -12,4 +12,4 @@ rule <step_name>__htseq_count:
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}"
"{params.command} -f bam -a {params.htseq_count_minaqual} -s {params.htseq_stranded} -r {params.htseq_orientation} {input.bam} {input.gff_file} 2> >(tee -a {log} >&2) > {output.stats}"
......@@ -7,7 +7,7 @@
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: "custom",
commands:
[
{
......
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