Not a valid project name: DEN-IM.nf

[TeacherHZ]

Hello, I encountered this problem when I entered the code. Is the file damaged?
N E X T F L O W ~ version 21.04.3
Not a valid project name: DEN-IM.nf

[cimendes]

Hello! Thank you for your interest in DEN-IM!

I've just cloned a new version and everything seems to be working well.

I've used the latest commit in the master.

$ git log | head
commit c47e6f1
Author: Inês Mendes cimendes@users.noreply.github.com
Date: Tue May 5 15:51:48 2020 +0100

What command are you using and where are you trying to run it? You're supposed to call DEN-IM.nf in the root of the repository, as exemplified in the README file.

single-end reads: nextflow run DEN-IM.nf --fastq="/path/to/input/files/*.fq.gz"
paired-end reads: nextflow run DEN-IM.nf --fastq="/path/to/input/files/*_{1,2}.fq.gz"

More information on how to run DEN-IM is available in the README or on our wiki

Let me know if you need further assistance :)

[TeacherHZ]

Hello! I am running in UABNTU, I installed NextFlow with Conda, and then cloned the code directly from Github, the running code is：
nextflow run DEN-IM.nf --fastq="out1.R1.fq.gz out1.R2.fq.gz"
nextflow run DEN-IM.nf --fastq="/path/to/input/files/out1.R1.fq.gz.fq.gz out1.R2.fq.gz"
They don't work, and the result is：
Not a valid project name: DEN-IM.nf
What should I do
thank you！

[TeacherHZ]

After I put den-im.nf into the home directory and run it, an error is reported：
Launching DEN-IM.nf [exotic_torricelli] - revision: d8505888f2
Script compilation error

• file : /home/heng/DEN-IM.nf
• cause: unable to resolve class Helper
  @ line 3, column 1.
  import Helper
  ^

Script compilation error

• file : /home/heng/DEN-IM.nf
• cause: unable to resolve class CollectInitialMetadata
  @ line 4, column 1.
  import CollectInitialMetadata
  ^

2 errors
I am a novice, did I not install Docker correctly？
thank you

[cimendes]

Hello!
After cloning DEN-IM, you need to go inside the repository folder and run DEN-IM from there.

Let's do it in steps!

1. Clone the DEN-IM repository to your machine
   https://github.com/B-UMMI/DEN-IM.git

2. Go inside the DEN-IM repository folder
   cd DEN-IM

3. Check that you see the correct files with ls. Here's how it's supposed to look like
   

4. Once you've made sure you're inside the DEN-IM repository directory, you can run it with the following command for paired-end data
   nextflow run DEN-IM.nf --fastq="/path/to/input/files/*_{1,2}.fq.gz"

[TeacherHZ]

Hello! It looks like this after I input ls

Then I type nextflow run DEN-IM.nf --help like this

my paired-end reads is out11.R1.fq.gz and out11.R2.fq.gz
I paste the two files into DEN-IM repository folder,Then run the code:
nextflow run DEN-IM.nf --fastq="/path/to/input/files/out11.R1.fq.gz.fq.gz out11.R2.fq.gz"
The result is:

No such file: /path/to/input/files/out11.R1.fq.gz.fq.gz out11.R2.fq.gz

-- Check script 'DEN-IM.nf' at line: 21 or see '.nextflow.log' file for more details
How should I enter my running code? Does the file to be run have to be put in DEN-IM repository folder?
thank you

[TeacherHZ]

It looks like this after entering ls

[TeacherHZ]

Hello! I installed Singularity using sudo apt install Singularity
Merge the paired-end reads sequence into the Den-im Repository Folder and run the code:
nextflow run DEN-IM.nf --fastq="D-DC11pear.assembled.fastq.gz"
结果是:


May I ask what causes this? Thank you

[cimendes]

Hello! Apologies for the very late reply! Unfortunately, this got lost in a bit of GitHub spam in my inbox. :(
Your issue seems to be related to singularity, and not with nextflow or the workflow. Please check what version of singularity you have installed. Nextflow documentation advises having version 2.3.x or higher (https://www.nextflow.io/docs/latest/singularity.html#singularity-docker-hub). Alternatively, you can give Docker a go. :)