Tomas Brabec
07/15/2024, 11:50 AMTomas Brabec
07/15/2024, 11:52 AMTomas Brabec
07/15/2024, 11:53 AMTomas Brabec
07/15/2024, 11:54 AMTomas Brabec
07/15/2024, 11:54 AMTomas Brabec
07/15/2024, 11:55 AMYucheng Zhang
07/15/2024, 7:28 PMC. H.
07/16/2024, 10:03 AMC. H.
07/16/2024, 10:04 AMC. H.
07/16/2024, 10:04 AMC. H.
07/16/2024, 10:04 AMRaquel Manzano
07/16/2024, 12:16 PMnf-core modules install strelka/germline
. My issue here is that I was trying to do this from a windows pc instead of my usual laptop that is a mac. I did the test from the mac, works well, I do it from the windows and starts to try to reinstall things because it says that modules are missing but present in module.json
, therefore tries to re-install and re-calcualte SHAs, which takes a long time and still hasn’t been able to finish. Is this a known windows issue?Alex Gibbs
07/17/2024, 11:09 AMchmod 777 work/*
and then re-running the pipeline using -resume
at the end then works, but we can’t seem to get to the root of the problem. Does anyone have any ideas? We have been consulting with our HPC team who are also struggling to understand why this is happening.
Any help is much appreciated!Ramiro Barrantes Reynolds
07/17/2024, 11:00 PMSimon Pearce
07/18/2024, 8:32 AMSlackbot
07/18/2024, 10:02 AMnservant
07/18/2024, 6:07 PMnextflow.config
, the command params.fasta = getGenomeAttribute('fasta')
will never work ...
Second, it seems that the new values I'm adding in the scope are not inherited the other (sub)workflows.
For instance, if I'm using params.fasta = getGenomeAttribute('fasta')
in the file <http://main.nf|main.nf>
I cannot run ch_fasta = Channel.fromPath( params.fasta )
in a subworkflow, as the params.fasta
value is not known.
If it's true, it means that all chanels related to the genome configuration must be created in the <http://main.nf|main.nf>
file and then passed to the other workflow ...
Thanks !Jasmin Frangenberg
07/19/2024, 10:09 AMuntar
causes a crash in the funcscan pipeline during an untar process that had worked before. More specifically, the nf-core/ubuntu:22.04
update (before it was 20.04) is the symptomatic cause.
The code UNTAR ( [ [], file('<https://card.mcmaster.ca/latest/data>', checkIfExists: true) ] )
fails now with the error:
tar (child): lbzip2: Cannot exec: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now
tar (child): cannot run bzip2: No such file or directory
tar (child): trying lbzip2
tar (child): lbzip2: Cannot exec: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now
Here is an example CI check. Any pointers to what to do except for not updating the untar
module? 😬Jay
07/19/2024, 3:20 PMnextflow run nf-core/rnaseq -r 3.14.0 -profile test -c nf-core/configs/nextflow.config --outdir /minitest/testRun
I am getting following error (quite reproducible on our server):
ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (1)'
Caused by:
Failed to pull singularity image
command: apptainer pull --name quay.io-biocontainers-qualimap-2.3--hdfd78af_0.img.pulling.1721401730658 <docker://quay.io/biocontainers/qualimap:2.3--hdfd78af_0> > /dev/null
status : 255
message:
INFO: Converting OCI blobs to SIF format
INFO: Starting build...
Copying blob sha256:53aaa050dfb057624a57ac4565e843b9d4bcf2b74de9bc36a115df3f90b943c3
Copying blob sha256:ca7680d1025d7a2df2c11bc7fdcc87594a7d0c43f16f970e7b0b4bef1b266918
Copying blob sha256:bd9ddc54bea929a22b334e73e026d4136e5b73f5cc29942896c72e4ece69b13d
Copying config sha256:bb400beef7dd58514e90def0cf426514bfe73be5d82ee846d7990e8b3cb10365
Writing manifest to image destination
FATAL: While making image from oci registry: error fetching image to cache: while building SIF from layers: conveyor failed to get: while getting config: no descriptor found for reference "b34cdfed77213ddb3b0444901a5725166a66328c24771dbd46c26d1045f26489"
-- Check '.nextflow.log' file for details
Thank you so much in advance for your help!Andrew VonHandorf
07/22/2024, 1:46 PMparamsSummaryLog
still shows the parameter's option as true. Is there a way to update this prior to nf-schema's validation of params that would allow the summary log to reflect the actual status of the parameter?nishant singh
07/22/2024, 4:47 PMnf-core create
tool (following these instructions: https://nf-co.re/docs/nf-core-tools/pipelines/create). As per the doc, I should be able to create a new pipeline by supplying a template.yml file using the --template-yaml
flag, however, I run into the following issue Error: no such option: --template-yaml
. Was this option removed from nf-core create?
I'm specifically trying to create a pipeline with a custom prefix (not nf-core/), which the linked doc above states is possible, but I'm unable to do that by supplying a template.yml file, or with a --prefix
flag.
Please let me know if there is a workaround for this, thank you!Nils Homer
07/22/2024, 5:38 PMscript:
used far more than shell:
in nf-core/modules
? What benefit does script:
have over shell:
?HamidKianGaikani
07/22/2024, 6:29 PMJames Kariuki
07/22/2024, 6:42 PMNicolás Alejandro Schcolnicov
07/22/2024, 9:30 PMJohn Arnn (DHHS)
07/23/2024, 4:31 PMdef args = task.ext.args ?: ''
To pass an argument to a module tool in an config file or even from the command line?
For example if I was running Sarek and wanted to pass the arguement '-noLog' to process SNPEFF_SNPEFF when it is call, how would I do that?Oluwasegun Isaac Daramola
07/23/2024, 5:20 PMCarson Miller
07/23/2024, 5:47 PMSlackbot
07/23/2024, 5:48 PMEduardo Horta
07/23/2024, 8:43 PM