README

Files Chromoseq.v9.wdl, application.new.conf, and LaunchChromoSeqFromCram.sh are for running locally (LSF) at MGI

Chromoseq_basespace.v9.wdl has all runtime attributes stripped, since the basespace cromwell workflow currently operates on a single node and is not configured to launch each job in a new container (this would waste resources- the current container already has everything each task needs to run)

launch_and_monitor_chromoseq.pl is for launching basespace from MGI

Instructions on running basespace and other information is written in https://confluence.ris.wustl.edu/display/CI/Basespace+SOP

forms & callbacks.js are configuration files from basespace that control the app input parameters and the command line instructions used to launch the app- these must be manually updated
current versions were last modified on 4/4/19
these can be accessed by logging in to the MGI organization and going to https://developer.basespace.illumina.com/apps/6984978/forms/revisions


launch_and_monitor_chromoseq.pl: finding constants

RefId
This was originally generated in project full_workflow_test1, analysis DRAGEN Reference Builder 03/28/2019 10:51:57
Analysis url: https://basespace.illumina.com/analyses/170755135?projectId=123592472
bs appsession get -i 170755135
bs list appresults --project-name=full_workflow_test1 --filter-field=AppSession.Id --filter-term=170755135
+-----------+---------------+----------------------------------------------+
|    Id     |     Name      |               AppSession.Name                |
+-----------+---------------+----------------------------------------------+
| 213691478 | all_sequences | DRAGEN Reference Builder 03/28/2019 10:51:57 |
+-----------+---------------+----------------------------------------------+
bs content appresult --id=213691478
+-------------+----------------------+
|     Id      |       FilePath       |
+-------------+----------------------+
| 14321367413 | all_sequences.v7.tar |
+-------------+----------------------+
The above ID is the value used in the workflow

ref_fasta
https://basespace.illumina.com/analyses/173645472?projectId=123592472
bs list appresults --project-name=full_workflow_test1 --filter-field=AppSession.Id --filter-term=173645472
+-----------+---------------+-----------------+
|    Id     |     Name      | AppSession.Name |
+-----------+---------------+-----------------+
| 216723517 | all_sequences | all_sequences   |
+-----------+---------------+-----------------+
bs content appresult --id=216723517
+-------------+------------------+
|     Id      |     FilePath     |
+-------------+------------------+
| 14477433053 | all_sequences.fa |
+-------------+------------------+