Has anyone on these fora successfully used Encode-DCCs pipelines? I am currently implementing their bulk RNA-seq pipeline, but I am finding the documentation incomplete in places, which complicates debuggining.
I was hoping to ask:
1) In default.conf, do you need to comment each variable you do not use, or should I leave them blank?
2) In the index.json files, does it matter in what order the arguments are given?
3) In the index.json files for single end sequencing, I cannot figure out from the documentation if I am supposed to leave out "rna.fastqs_R2" : [], or leave the line in there as an empty array?
4) If I provide an absolute path for all data and reference files, does it matter where there are stored?
5) If anyone could send me working versions of these files, would also greatly simplify the process.
6) I'm not married to any software versions - could switch; but I am currently using:
Python v3.8.4 Java v11.0.2 Singularity v2.5.2 Caper v2.1.2
Thank you!
