Chip.wdl has a limitation of 6 replicates

[GFrosi]

Hi,

I am trying to run the ENCODE pipeline for 12 traits samples and 20 controls on HPC. The pipeline worked (I am using the piperunner.sh code and slurm-singularity as backend from IHEC / integrative_analysis_chip), however I just have the outputs for 6 replicates (the 6 first described in the Input.json). I checked the chip.wdl file and in fact the pipeline has a "restriction" of 6 replicates:

fastqs Array[File] fastqs_rep1_R1 = [] # [merge_id] Array[File] fastqs_rep1_R2 = [] # do not define _R2 array if your sample is not paired end Array[File] fastqs_rep2_R1 = [] # do not define if you have a single replicate Array[File] fastqs_rep2_R2 = [] # do not define _R2 array if your sample is not paired end Array[File] fastqs_rep3_R1 = [] # do not define if you have <=2 replicates Array[File] fastqs_rep3_R2 = [] # do not define _R2 array if your sample is not paired end Array[File] fastqs_rep4_R1 = [] # do not define if you have <=3 replicates Array[File] fastqs_rep4_R2 = [] # do not define _R2 array if your sample is not paired end Array[File] fastqs_rep5_R1 = [] # do not define if you have <=4 replicates Array[File] fastqs_rep5_R2 = [] # do not define _R2 array if your sample is not paired end Array[File] fastqs_rep6_R1 = [] # do not define if you have <=5 replicates Array[File] fastqs_rep6_R2 = [] # do not define _R2 array if your sample is not paired end Array[File] ctl_fastqs_rep1_R1 = [] # [merge_id] Array[File] ctl_fastqs_rep1_R2 = [] # do not define _R2 array if your sample is not paired end Array[File] ctl_fastqs_rep2_R1 = [] # do not define if you have a single control Array[File] ctl_fastqs_rep2_R2 = [] # do not define _R2 array if your sample is not paired end Array[File] ctl_fastqs_rep3_R1 = [] # do not define if you have <=2 controls Array[File] ctl_fastqs_rep3_R2 = [] # do not define _R2 array if your sample is not paired end Array[File] ctl_fastqs_rep4_R1 = [] # do not define if you have <=3 controls Array[File] ctl_fastqs_rep4_R2 = [] # do not define _R2 array if your sample is not paired end Array[File] ctl_fastqs_rep5_R1 = [] # do not define if you have <=4 controls Array[File] ctl_fastqs_rep5_R2 = [] # do not define _R2 array if your sample is not paired end Array[File] ctl_fastqs_rep6_R1 = [] # do not define if you have <=5 controls Array[File] ctl_fastqs_rep6_R2 = [] # do not define _R2 array if your sample is not paired end

Is there any solution to run more than 6 replicates?

Thanks in advance for your help, Gabriella Frosi

[leepc12]

Please use the latest pipeline which supports up to 10 replicates.

[GFrosi]

Hi @leepc12 Thanks for your answer, Unfortunately I have an arbitrary number of replicates (often more than 10).

Is there a way to use the pipeline with more than 10 (indeed any number of replicates)?

Thanks

[leepc12]

No. If those replicate have any concordance then run a separate pipeline for each replicate. i.e. rep1 only.

[GFrosi]

Hi @leepc12, Thanks a lot.