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bwameth index creation fails #352
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Hey, Issue description:I am having the same issue reported here when I am trying to repeat the analysis using TestThe following test works fine nextflow run nf-core/methylseq --aligner bwameth --outdir $RefDir -profile test,conda Summary of my experimental conditions:
Command used and error message:Pipeline InfoN E X T F L O W ~ version 23.10.0
I have tried including and excluding the following flags, but no version has worked:
I appreciate any help! :) Maximiliano |
Mmm, I guess I found the problem. You need to provide the 2 indexed versions of the genome
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I disagree. You've found your way around the bug by providing more inputs, meaning that the pipeline did not need to create them. However, the pipeline should automatically generate the index files itself if only given a Fasta file. This is what we need to fix:
Looks like there's something wrong with how the channels are being built / supplied. |
Hi, I also encountered the same issue when trying to run |
Has this been fixed? I'm still having the same error when trying to use bwameth as the aligner |
@drothen15 Not sure if a fix has been included in a release yet, but I was able to fix this locally by modifying the In the I resolved it by removing the tuple altogether, and then updating the One solution (that I used):
instead of
And then modifying
instead of
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Sorry, I have a doubt: is the input to Thank you! |
I think the later, for me that's how I got it to work |
a fix for this issue has been added to the dev branch. could someone test it and let us know so we can mark this issue closed if successful |
Description of the bug
Hi.
I'm encountering an error with the methylsig pipeline when using bwameth aligner. The pipeline runs fine with Bismark, but my mapping is low (~40%) and I want to compare against bwameth.
The error seems to be in preparing the reference genome index. I tried saving the reference genome locally and running offline, but encounter the same issue. Tried with both methylsig 2.4.0 and 2.5.0.
Command used and terminal output
Relevant files
nextflow.log
System information
Nextflow version 23.04.3
HPC, LSF executor
nf-core/methylseq 2.4.0 and 2.5.0
Singularity container
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