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epi2me-labs / wf-clone-validation

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Cannot invoke method contains() on null object #1

Closed IFIK-virology closed 2 years ago

IFIK-virology commented 2 years ago

Using the input basic parameters for "wf-clone-validation", I repeatly get the following error both on a mac and Ubuntu machine. What could the problem be?

N E X T F L O W  ~  version 21.04.3
Launching `epi2me-labs/wf-clone-validation` [amazing_visvesvaraya] - revision: 4048ddebdc [master]
Cannot invoke method contains() on null object

 -- Check script '/home/c3po/.nextflow/assets/epi2me-labs/wf-clone-validation/main.nf' at line: 473 or see '.nextflow.log' file for more details
sarahjeeeze commented 2 years ago

Thanks for pointing this out. It is likely that due to lack of information in the help message you are missing the --db_directory parameter, you may also need to download the required database by using the following cmd.

wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-clone-validation/wf-clone-validation-db.tar.gz
tar -xzvf wf-clone-validation-db.tar.gz

We will update the --help message to make this clearer to future users.

IFIK-virology commented 2 years ago

Tnx! Does seems to do the trick.

Bw, Ronald

From: Sarah Griffiths @.> Reply to: epi2me-labs/wf-clone-validation @.> Date: Thursday, 28 October 2021 at 11:35 To: epi2me-labs/wf-clone-validation @.> Cc: Ronald Dijkman @.>, Author @.***> Subject: Re: [epi2me-labs/wf-clone-validation] Cannot invoke method contains() on null object (Issue #1)

Thanks for pointing this out. It is likely that due to lack of information in the help message you are missing the --db_directory parameter, you may also need to download the required database by using the following cmd.

wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-clone-validation/wf-clone-validation-db.tar.gz

tar -xzvf wf-clone-validation-db.tar.gz

We will update the --help message to make this clearer to future users.

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