The documentation suggests that multiple bam files can be analysed by the pipeline, however, this did not work for me. I was only able to run one bam file at a time.
-b /bam_files/*.bam
This did not work. It says that it doesn't understand the command line arguments and then prints out the list of filenames.
-b /bam_files/myfirstdataset.bam did work fine.
So I had to run a for loop in bash to analyse all my datasets.
The documentation suggests that multiple bam files can be analysed by the pipeline, however, this did not work for me. I was only able to run one bam file at a time.
-b /bam_files/*.bam
This did not work. It says that it doesn't understand the command line arguments and then prints out the list of filenames.
-b /bam_files/myfirstdataset.bam did work fine.
So I had to run a for loop in bash to analyse all my datasets.