After finishing a pipeline run I wanted to change the cDNA file to trigger a rerun of salmon, but this also triggered a restart of Hisat because of the rule check_annotation_files. Given that the cDNA is not relevant for Hisat2 mapping I propose a more fine-grained solution that separately checks GTF vs DNA and GTF vs cDNA.
After finishing a pipeline run I wanted to change the cDNA file to trigger a rerun of salmon, but this also triggered a restart of Hisat because of the rule
check_annotation_files
. Given that the cDNA is not relevant for Hisat2 mapping I propose a more fine-grained solution that separately checks GTF vs DNA and GTF vs cDNA.For now, I can circumvent the rerun by using: