phoenix | Jetstream compatible workflow template | Genomics library
kandi X-RAY | phoenix Summary
kandi X-RAY | phoenix Summary
This workflow supports the analysis of human sequencing samples against the GRCh38 reference genome using ensembl version 98 gene models. The workflow is designed to support project level analysis that can include one or multiple types of data. Though not required the expectation is a project contains data from a single individual thus centralizing all data types in a standardized output structure. The workflow template supports a diverse array of analysis methods required to analyze DNA, RNA, and single cell data. Based on standardized variables it also supports integrated analysis between data types. For some processes multiple options are provided that can be individually enabled or disabled by configuration parameters. Like all JetStream (workflows developed at TGen this workflow is designed to facilitate our dynamic and time sensitive analysis needs while ensuring compute and storage resources are used efficiently. The primary input is a JSON record from the TGen LIMS but hand created inputs in the form of a JSON or EXCEL worksheet can also be provided when run manually or by submission to the related JetStream Centro (web portal. All required files defined the the pipeline.yaml can be created using code provided in the JetStream Resources repository (
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Top functions reviewed by kandi - BETA
- Check for unique contigs
- Uses samtools to get frags using samtools
- Gets the number of reads in a region
- Calculates the length of a cigar string
- Extract data from a samtools markdown file
- Add samples to a json object
- Start processing
- Process a single variant record
- Return the index of a sample column in a given variant
- Convert a bam file to a pandas dataframe
- Add metrics to Picard
- Extend the segments
- Process VCF files and return new VCF records
- Process command line arguments
- Generate summary table
- Parse arguments and validate them
- Parse Picard stats from a Picard file
- Write a new VCF file
- Parse arguments
- Extracts cellranger metrics data
- Add histogram data to a dictionary
- Make calls for a given sample
- Extract histogram data from a Picard file
- Verify BAM id extraction
- Performs a HTTP request
- Returns the location of the output file
phoenix Key Features
phoenix Examples and Code Snippets
{
"project": "",
"study": "",
"email": "",
"hpcAccount": "",
"isilonPath": "",
"pipeline": "phoenix",
"dataFiles": [],
"dnaAlignmentStyle": "tgen",
"email": "somebody@tgen.org",
"isilonPath": "",
"pipeline"
"dataFiles": [
{
"assayCode": "TPFWG",
"dnaRnaMergeKey": "GIAB_NA12878_1_CL_Whole",
"fastqCode": "R1",
"fastqPath": "/home/tgenref/homo_sapiens/control_files/giab/fastq/NA12878_140407_D00360_0016_ASUPERFQS01/Projec
Project
|--GeneralLibaryType
| |--AnalysisType
| | |--Tool
| | | |--SampleName
| | | |--ResultFiles
| | |--Tool
| |--AnalysisType
|--GeneralLibaryType
Community Discussions
Trending Discussions on phoenix
QUESTION
I'm trying to use moment.js
to get the correct date and time of a user ignoring the date and time from the local computer which I'm thinking the user might change sometime. It's there a way to achieve this, I'm currently using the code below but it's not getting me the results I need
ANSWER
Answered 2021-Jun-14 at 13:35An easy way of doing this is using an external service to return a time that you want, either by creating an api yourself or using an existing one.
If you want something fast and easy you can try TimeAPI.
QUESTION
I'm trying to pass data from a tableView when the cell is tap to a detailTableView. I'm not getting any errors when the detail tableView is loaded. The segue is being performed, however, the tableView remains blank. My goal to add the color to the textLabel in the cell and add the zord in the detailTextLabel within the same cell. Can someone tell me what I'm doing wrong
...ANSWER
Answered 2021-Jun-14 at 08:17May be order here matters performSegue
should be before deselectRow
for if let index_path = self.table_View.indexPathForSelectedRow {
to have a value
QUESTION
I have a list of objects named rides and I want to get the time and date fields and want to sort the data in ascending order
...ANSWER
Answered 2021-Jun-12 at 11:56You can use Array#sort
and parse the date
and time
of each element in a Date
object for comparison:
QUESTION
I have an issue regarding SQL stored procedures. I have connected my SQL Server db to my ASP.NET Web Forms app and have created a button that uses Stored Procedures to Save data inside the db.
I only want to use two fields on my front-end, namely Name and Surname. I do not want other moderators to input the Id (which is the primary key), so the stored procedure must increment it by itself once they add some Name and Surname.
However, once data has been put in the fields, all rows get populated with that data?
Example database.
Id Name Surname 1 Alex Smith 2 Bob Phoenix 3 Correy LollasAfter clicking on the Insert button I have created populating Name and Surname (Id is supposed to autoincrement)
Id Name Surname 1 Test Name 2 Test Name 3 Test NameStored procedure, although I think the problem is in the logic.
...ANSWER
Answered 2021-Jun-07 at 13:58The answer was to change @Id int = NULL
to @Id int
and also just WHERE ([Id] = @Id)
. Now everything is working as it should.
Full:
QUESTION
ANSWER
Answered 2021-Jun-07 at 13:42The expected JSON result from your question is not the same as the JSON from the API!
You can use states.items.filter
instead of states.filter
but the API linked has no property abbr
so it will return undefined:
QUESTION
I have a table with a list of contacts as seen in the image. I also have an event that gets triggered when a row is clicked so it can show the selected contact detail (I am using angular NGIF directive to show and hide the detail)
The thing is because my google input is placed inside an NGIF block, when user expands the contact detail and tries to type in it, the predictions (pac-container) is showing on the row that I clicked (within the table) rather than underneath the google input autocomplete search box.
I tried to manipulate the css of the class pac-container
but I couldn't figure out a way to override the css of that class.
Here is my the html of my autocomplete search box
...ANSWER
Answered 2021-Jun-06 at 18:45I had to go with a DOM Manipulation way using JS.. so I added a (keyUp) event handler on google search box with a method to calculate the position like the following:
QUESTION
Python newbie here. I'm looking at some daily weather data for a couple of cities over the course of a year. Each city has its own csv file. I'm interested in comparing the count of daily average temperatures between two cities in a bar graph, so I can see (for example) how often the average temperature in Seattle was 75 degrees (or 30 or 100) compared to Phoenix.
I'd like a bar graph with side-by-side bars with temperature on the x-axis and count on the y-axis. I've been able to get a bar graph of each city separately with this data, but don't know how to get both cities on the same bar chart with with a different color for each city. Seems like it should be pretty simple, but my hours of search haven't gotten me a good answer yet.
Suggestions please, oh wise stackoverflow mentors?
Here's what I've got so far:
...ANSWER
Answered 2021-May-29 at 19:32You can concat
DataFrames, assign
ing city as a column, and then use histplot
in seaborn
:
QUESTION
I'm using EEx template engine to render HTML pages (no Phoenix here). I'm passing the connection (Plug.Conn
) conn
to the template along with extracted parameter list (params
) and the session map (session
) with : body = EEx.eval_file(path, conn: conn, params: conn.params, session: session)
. params
and session
are provided just for convenience as they also are in the connection.
If the page modifies the session (configured with cookies), say with something like <% Plug.Conn.put_session(conn, "reply", 42) %>
), this modifies the connection but this also remains local to the page and is not propagated.
Is there a way to retrieve this modified version of the connection from the EEx engine ?
NB: I'm talking about the connection (Plug.Conn
), but it could be any variable that is modified or created by the template engine, just a similar way Code.eval_string("a=1\n b=2\n c=a+b")
does : {3, [a: 1, b: 2, c: 3]}
.
ANSWER
Answered 2021-May-25 at 15:13EEx.eval_file
and EEx.eval_string
both return a String
type, they do not return the updated bindings (as, like you say, Code.eval_string
does).
I think the reasoning behind this is that you want a render
function to have no side-effects (like database calls or session modification).
You don't want business-logic in your templates, you want to put that in your controller or data layer (with the advantage that you can test it in isolation).
Maybe offtopic, but if you're coming from a PHP background (where you can put all your code in one file that looks like an HTML template) this might be the source of the confusion.
UpdateThis could work though:
QUESTION
I know this is probably a basic question, but I'm just getting into GUI building and haven't needed to dabble much in classes for that matter. I have some code (see below) to handle the GUI portion of the program (the CLI version is already running perfectly, but management runs for the hills whenever they see a CLI...), but I can't quite get it to work out. FYI running python 3.9.1 and wxPython 4.1.1 Phoenix (though wx.version
also spits out wxWidgets 3.1.5
, if that's relevant) on Windows 10
A lot of the code was based around examples / other folks asking stuff here, and unfortunately I can't find the original posts to credit them, but this is really just for learning and once I have a grasp of what I'm doing I'll be writing everything from scratch. So to the original authors, I apologize, but I thank you enormously!
The program is to display a "start" screen (frame), with just a title and single button. On clicking the button, a modal file dialog box opens where the user selects the .csv data file to use, the start frame disappears, and a new frame appears with a view of the data in the right pane (in a grid sizer) and some drop downs and radio buttons in the left pane. The last drop-down (self.inputNum
) will be bound to an event handler which will add a number of additional drop-downs for the user to select the different targets to analyze (the number of course being determined by their selection in the self.inputNum
combobox). However, when running the script, I get an error
ANSWER
Answered 2021-Apr-28 at 17:12Sorry folks, my pre-coffee brain was calling CreateGrid()
when the function is defined as createGrid()
. There were a few other mistakes in the code (event handlers that referred to buttons that I no longer had implemented, calling StartFrame.makeMenuBar
from a different class without also importing the functions StartFrame.makeMenuBar
called, etc).
But still feel free to point out inefficiencies and redundancies and other various un-pythonic things I'm doing. Still learning :)
QUESTION
In the project I have phoenix web app which serves its own frontend (webpack 5, served on "/")
...ANSWER
Answered 2021-May-27 at 14:51Did you tried the following structure for your Nuxt app?
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