Need some more explanation about config and usage

[cfljam]

A few comments:

A few issues I encountered:

1. there needs to be some clarification of what config files are and which we edit. I was confused by

config: Location of config file ["$baseDir/design.config"]

I think this parameter is meant to be design since the corresponding entry in Nextflow.config is:

design = "./design.config"

So do we edit the design.config and Nextflow.config file per project then tweak per run by passing in parameters???
2. I think rep needs to be explained from the design file. Does this mean that reps are eg runs of the same sample across different lanes so that appropriate read groups can be assigned within samples?
3. Monitoring of a run. How can we determine status of our run?
4. Default ploidy value in the master config file should be 2
5. How to stop, restart run?
6. Best practices for reproducibility. How can I best track how I generated data?

[cfljam]

HI @hdzierz My current working efforts are in a bash notebook see https://gist.github.com/cfljam/4f62e280691a8f5bcdf2781a85596a5a

I think for kiwifruit it would be ideal to work through generating variant calls from the published HongYang fastq

[cfljam]

also another question is why the workflow creates the align_HW* samples which were not in my sample set?

(py3r-env) [08:24][cfljam@aklppf31:10.PoolSeq (master)] $ ls -l AlignEnsemblBol/220.align/
total 36071515
-rw-rw-r--. 1 cfljam powerplant     217614 Sep 12 07:58 align_HW1_1.bam
-rw-rw-r--. 1 cfljam powerplant     217627 Sep 12 07:58 align_HW2_2.bam
-rw-rw-r--. 1 cfljam powerplant 6561393676 Sep 12 07:59 align_Pool1_1.bam
-rw-rw-r--. 1 cfljam powerplant 5631820747 Sep 12 07:58 align_Pool2_1.bam
-rw-rw-r--. 1 cfljam powerplant 5226315349 Sep 12 07:58 align_Pool3_1.bam
-rw-rw-r--. 1 cfljam powerplant 7561486315 Sep 12 07:59 align_Pool4_1.bam
-rw-rw-r--. 1 cfljam powerplant 5723608296 Sep 12 07:58 align_Pool5_1.bam