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Cutadapt set -m=1 to avoid empty reads

CJHerrmann requested to merge cutadapt_min_len into dev

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.
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)

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