closes #161 (closed)
Cutadapt's default behavior is to keep all reads, even if they are empty after adapter removal. However, STAR will fail if encountering empty reads.
Solution:
Add -m=1 to all cutadapt rules, before the additional parameters from rule_config.yaml are inserted. Like this, if no rule_config.yaml is specified, -m=1 will be used, otherwise it will be overwritten by the value from rule_config.
The following tests have been performed locally:
confirm that cutadapt uses the second parameter value if a parameter is specified twice (tested with toy file in command line cutadapt call)
Specify the whole sequence of first read from input file as 3' adapter in the samples.tsv and run zarp with and without rule_config (This failed prior to adding -m=1)
Not tested:
cluster execution
whether the second value of -m is also used when cutadapt is called from snakemake (and not directly from command line)
