Open cfljam opened 8 years ago
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
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
A few comments:
A few issues I encountered:
I think this parameter is meant to be design since the corresponding entry in Nextflow.config is:
So do we edit the design.config and Nextflow.config file per project then tweak per run by passing in parameters???