BUG: inconsequential CLI changes prompt reruns

[siebrenf]

Describe the bug Changing the number of cores should not prompt reruns.

I'll add other options to the list if I find them.

[siebrenf]

-r -k --snakemakeOptions untill=[] are fine. --snakemakeOptions omit_from=[] prompts a rerun.

[Maarten-vd-Sande]

Ah good catch! Does it re-run everything or a small-ish selection/branch only (e.g. qc report)? I can imagine params like this causes the qc stuff to be re-run. Seems like we need a config parsing function for this :see_no_evil:

https://github.com/vanheeringen-lab/seq2science/blob/master/seq2science/rules/qc.smk#L502

I would expect both snakemakeoptions to cause the same behavior

[siebrenf]

these rules use threads in their params:

• bam2cram
• fastp_SE
• fastp_PE
• samtools_presort
• samtools_sort

these rules seem to get params changes listed:

• multiqc_explain
• multiqc_header_info
• multiqc_samplesconfig

Finally, the fastp and samtools_presort rules seem to get marked all the time, even when threads are removed from the params. Could this be related to the temp()?

[Maarten-vd-Sande]

I think you've solved this right?