Thanks for providing the snakemake pipeline. I am unfamiliar with the snakemake syntax. I encountered a problem when running the pipeline at the intra-sample merging step. I imagine this is for samples sequenced in different platforms? For my samples, I only have one fastq input file for each sample. Do you have recommendations on how to disable all the intra-sample merging step? This will create problems in samtools merge step because it expects more than one sample. I tried to remove the rule directly but it caused more problems.
Hi,
Thanks for providing the snakemake pipeline. I am unfamiliar with the snakemake syntax. I encountered a problem when running the pipeline at the intra-sample merging step. I imagine this is for samples sequenced in different platforms? For my samples, I only have one fastq input file for each sample. Do you have recommendations on how to disable all the intra-sample merging step? This will create problems in samtools merge step because it expects more than one sample. I tried to remove the rule directly but it caused more problems.
Thanks, Wei