A number of commands produce silently extra files not defined in the rule output section.

When I try to make sure these are produced by adding them to 'rule all:' a re-run of the workflow fails because the file are not found in the rule(s) output list.

Can I add a supplementary file (not present as {output}) to the 'rule all:'?

Thanks

eg: STAR index produces a number of files in a folder defined by command arguments, checking for the presence of the folder does not mean that indexing has worked out normally

added for clarity, the STAR index exmple takes 'star\_idx\_75' as output argument and makes a folder of it in which all the following files are stored (their number may vary in function of the index type).

```
chrLength.txt
chrName.txt
chrNameLength.txt
chrStart.txt
exonGeTrInfo.tab
exonInfo.tab
geneInfo.tab
Genome
genomeParameters.txt
SA
SAindex
sjdbInfo.txt
sjdbList.fromGTF.out.tab
sjdbList.out.tab
transcriptInfo.tab

```

What I wanted was to check that they are all present BUT none of them is used to build the command itself and if I required them in the rule all: a rerun breaks because they are not in any snakemake {output} definition.

This is why I asked wether I could create 'fake' output variables that are not 'used' for running a command but allow placing the corresponding items in the 'rule all:' - am I more clear now :-).