debug htseq-count

tools/htseq_count/htseq_count.rule.snakefile

@@ -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}"

tools/htseq_count/htseq_count.yaml

@@ -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:
     [
       {