Thanh Giang Nguyen Tan

### Debug output ``` Vagrant failed to properly resolve required dependencies. These errors can commonly be caused by misconfigured plugin installations or transient network issues. The reported error is: nokogiri...

I found that on this repo, the team has the role for nis_client. But it seems to not be ready to run on any playbook. Do I miss something or...

Endpoint url error

5

## Bug report Nextflow file main.nf ``` #!/usr/bin/env nextflow params.values = Channel.from(1) process echoValue { publishDir "${params.outdir}/echoValue/", mode: 'copy' input: val value output: path "*_echoValue.txt" script: """ echo "Value: $value"...

In the applet, I define the input is the array:file with optional is true. When I use the dxni command to generate the wdl file to import to the workflow....

The HiC data published by NG2019 seems miss the resolution at chr9. I check on the latest version with this https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/blob/main/workflow/scripts/juicebox_dump.py or the old version with with branch NG2019 #Download...

Duplicate score_column in `predict.py`

1

This one is already defined in the argument of the command line, I think if the hic file does not exist, it will return the "" for hic params. https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/blob/main/workflow/rules/predictions.smk#L10C3-L10C41

Correct the MS ID for Lys-C in the dataset PXD007073

1

I found that there is an issue related to MS. It seems the curator using excel or sheet to automate the MS ID, however, instead of auto copying the first...

I launch the galaxy server, there is a local tool using the docker. However, with the option mounting docker socket to the docker and add the PARRENT_DOCKER=True seems work only...

Configure S3 for units.tsv

4

I upload the input file to the remote S3 bucket. I have this units.tsv as below and correctly used put the S3 credential in the config file. However, it seems...