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Thanks for your contribution, I want to refer to your process to implement it step by step, but I can't find the detailed use method, software and workflow，such as smtools、bismark、or piard???
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## **Describe the bug**
when i append the tss file ,it show this mistake
## **OS/Platform**
- Caper version: 2.1.3
## **Caper configuration file**
2022-04-11 21:37:00,784|caper.cli|INFO| Crom…
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**Describe the bug**
As was brought up in the Dockstore Slack, when I run a WDL on the Dockstore CLI, files are created all over the place. It doesn't seem intended for the Dockstore CLI to put output…
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As discussed in https://github.com/broadinstitute/cromwell/issues/6235, developers of workflows for GCP who store their images in Google Container Repositories can be exposed to large Google GCS egres…
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**Describe the bug**
Due to the nature of this bug I can't be sure if it still exists in 1.10.0, but it does exist in 1.9.0 so it might be worth looking into. Basically, when using Dockstore's recomme…
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Hi, team!
I am trying the chip-seq-pipeline2 and atac-seq-pipeline using "local" backend.
Both the pipeline stalled at "task=chip.read_genome_tsv:-1, retry=0, status=WaitingForReturnCode".
About …
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Also see discussions here: https://github.com/openwdl/wdl/discussions/408
Currently, it is specified that the task command block is executed by a bash interpreter. Non-bash languages are supported ei…
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Many tools get input files and create the output files in the same folder as the input instead of the execution folder, as a result, I have nothing in execution folder but in the input folder I have a…
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Exception thrown on pipeline launch, seems to be a Caper problem (get same output when running caper without input JSON). Running on SLURM cluster with pipeline v1.8.0.
**Caper configuration file**…
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### Describe the bug 🐞
We are using an echo command to get the `bwa` version and that can fall out of sync when the docker is updated.
https://github.com/CDPHE-bioinformatics/CDPHE-RSV/blob/9bdf…