I would like to start with this issue but preseq modules such as ccurve or lcextrap use BAM files as input; what should the strategy be to include this? Should the pipeline accept a sample sheet of BAM files instead of FASTQ files? And depending on the type of samplesheet follow a differential flow: FASTQ as input: fastqc, multiqc, etc || BAM as input: preseq, multiqc, etc?
I would like to start with this issue but preseq modules such as ccurve or lcextrap use BAM files as input; what should the strategy be to include this? Should the pipeline accept a sample sheet of BAM files instead of FASTQ files? And depending on the type of samplesheet follow a differential flow: FASTQ as input: fastqc, multiqc, etc || BAM as input: preseq, multiqc, etc?