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QUESTION
I am writing a snakemake pipeline to eventually identify corona virus variants.
Below is a minimal example with three steps:
...ANSWER
Answered 2021-Jun-10 at 07:54I think the problem is that rule catFasta
doesn't contain the wildcard barcode
. If you think about it, what job name would you expect in {wildcards.barcode}.{rule}.{jobid}
?
Maybe a solution could be to add to each rule a jobname
parameter that could be {barcode}
for guppyplex
and minion
and 'all_barcodes'
for catFasta
. Then use --jobname "{params.jobname}.{rule}.{jobid}"
QUESTION
I am writing a snakemake to produce Sars-Cov-2 variants from Nanopore sequencing. The pipeline that I am writing is based on the artic network, so I am using artic guppyplex
and artic minion
.
The snakemake that I wrote has the following steps:
- zip all the
fastq
files for all barcodes (rulezipFq
) - perform read filtering with
guppyplex
(ruleguppyplex
) - call the
artic minion
pipeline (ruleminion
) - move the stderr and stdout from qsub to a folder under the working directory (rule
mvQsubLogs
)
Below is the snakemake that I wrote so far, which works
...ANSWER
Answered 2021-Jun-08 at 15:40The rule that fails is rule guppyplex
, which looks for an input in the form of {FASTQ_PATH}/{{barcode}}
.
Looks like the wildcard {barcode}
is filled with barcode49/barcode49.consensus.fasta
, which happened because of two reasons I think:
First (and most important): The workflow does not find a better way to produce the final output. In rule catFasta
, you give an input file which is never described as an output in your workflow. The rule minion
has the directory as an output, but not the file, and it is not perfectly clear for the workflow where to produce this input file.
It therefore infers that the {barcode}
wildcard somehow has to contain this .consensus.fasta
that it has never seen before. This wildcard is then handed over to the top, where the workflow crashes since it cannot find a matching input file.
Second: This initialisation of the wildcard with sth. you don't want is only possible since you did not constrain the wildcard properly. You can for example forbid the wildcard to contain a .
(see wildcard_constraints
here)
However, the main problem is that catFasta
does not find the desired input. I'd suggest changing the output of minion
to "nanopolish/{barcode}/{barcode}.consensus.fasta"
, since the you already take the OUTDIR from the params, that should not hurt your rule here.
Edit: Dummy test example:
QUESTION
I need to create a node.js app that connects to this ftp server and downloads files from this directory:
ftp://www.ngs.noaa.gov/cors/rinex/2021/143/nynb
I've tried following the ftp
npm package docs but I feel like I am doing something horribly wrong:
ANSWER
Answered 2021-May-23 at 08:12There are a few points :
- You're connecting to the local ftp with
c.connect();
. You need to connect towww.ngs.noaa.gov
to download files from there. - This path
cors/rinex/2021/143/nynb
is a directory on the remote host.c.get
doesn't work, you need to list all files in the directory then download them 1 by 1.
The code below connect to the remote server and list all files in the directory
QUESTION
I am using snakemake in cluster mode to submit a simple one rule workflow to the HPCC, which runs Torque with several compute nodes. The NFSv4 storage is mounted on /data. There is a link /PROJECT_DIR -> /data/PROJECT_DIR/
I submit the job using:
...ANSWER
Answered 2021-Apr-01 at 11:12Solved by providing a jobscript (--jobscript SCRIPT
) with:
QUESTION
To install this library, run:
...ANSWER
Answered 2021-Apr-01 at 08:14The answer is here:
Module '"../../node_modules/ngx-device-detector/ngs-device-detector"' has no exported member 'Device Detector Module'.
It means that the library does not have the DeviceDetectorModule
. You're probably using old documentation.
In the library docs it states that now you can use the service directly, without the module:
QUESTION
i got a file formatted like that : (each space = tab separator)
...ANSWER
Answered 2021-Feb-08 at 11:01With your shown samples, could you please try following. Written and tested in GNU awk
.
QUESTION
I am working on a little showcase that is supposed to demonstrate how you can write interactive programs in a purely functional manner using functional-reactive programming (specifically RxJava2).
My goal is to create a simple interactive game. The main function of the game (let's call it Next Game State, or NGS for short) takes the current state of the game, a user input, as well as a random number and computes the next state of the game from those three inputs. Fairly straightforward so far. The user inputs and the random numbers are Flowable
s that were created from Iterable
s or via generators. I envisioned that the game state itself would be a Flowable as well (but I might be wrong about that).
I am struggling to find the right functional-reactive operator that applies the function to the three inputs and produces the next state of the game. Initially, I thought that Flowable.zip(source1, source2, source3, zipper)
would be right operation: it could take the three flows and combine it via the NGS function into a new Flowable. That, unfortunately, does not account for the fact that the resulting Flowable itself needs to be one of the inputs of the zip operation, which seems an impossible setup. My next idea was to use Flowable.generate
, but I need the two additional inputs from other Flowable
s to calculate the next state, and there is no way to feed those into the generate
operator.
In a nutshell, I'm trying to realize something similar to this (pseudo-)marble diagram:
...ANSWER
Answered 2021-Jan-06 at 09:57The user-input and randome number are two separate streams, which could emit at any time by their own.
Solutionlong story short, is there an existing operator that supports this behavior?
Yes, there is. You could use #scan(seed, { current, upstream
. -> newValue }
QUESTION
I am fairly familiar with R, but have 0 experience with web scraping. I had looked around and cannot seem to figure out why my web scraping is "failing." Here is my code including the URL I want to scrape (the ngs-data-table to be specific):
...ANSWER
Answered 2020-Nov-28 at 03:58The content of that table is generated dynamically: check it by saving the page from your browser (or, with your code, write_html(webpage,'test.html')
) and then opening the saved file. So you probably can't capture it with rvest
. Browser simulation packages like RSelenium
will solve the problem.
QUESTION
I have two Azure functions, one is running on Premium plan that gives me "Outbound IP addresses"
while the second one is running on consumption plan that only gives me "Virtual IP address"
. Below are screen-shots from their properties tab.
I have Network Security Group for which I am trying to only allow Inbound traffic from these two azure functions. I have updated the NGS policy with "Outbound IP address" of the Premium Azure function, as well as the "Virtual IP Address" of Consumption plan.
The premium function is able to communicate with the Network Security group afterwards, however, I am not able to get it to work for the Consumption plan.
Is there a way I can get the "Outbound IP address" for functions running on Consumption plan?
...ANSWER
Answered 2020-Oct-23 at 09:09What are the options I have to get this working?
In Azure, Azure functions hosting on a different hosting plan have different features. Outbound IP restrictions do not support in the Consumption plan. It does not directly expose the outbound IP addresses of the function app. You can not add the "Virtual IP Address" of the Consumption plan. You could add the possibleOutboundIpAddresses of the Function app into the inbound of NSG rules.
However, the possible outbound IP address list may change or update.
When a function app that runs on the Consumption plan or the Premium plan is scaled, a new range of outbound IP addresses may be assigned. When running on either of these plans, you may need to add the entire data center to an allow list.
QUESTION
I'm working with Pandas and I have a big part list with Main Assy, Sub Assy I, Sub Assy II and Sub Assy III. Only one "Assy" column per row can be filled with a string in the dataframe. The aim is to transfer the arrangement of the parts into a numbering system.The following table shows the expected outcome:
...ANSWER
Answered 2020-Oct-29 at 18:53The change of output to be applied over each row can be fully determined by the current "level" and the previous level. Here "level" means the index number of the column having a non-zero entry.
In other words, a state variable retaining the level of the previous row is sufficient for populating the current row correctly.
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