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nf-core / atacseq

ATAC-seq peak-calling and QC analysis pipeline
https://nf-co.re/atacseq
MIT License
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zipped fasta file doesn't work #277

Closed rodriguesk closed 1 year ago

rodriguesk commented 1 year ago

Description of the bug

I’m getting this error and I’m wondering how to solve it. I’m using the genome mm39 (which is new and not in igenome) so I’m trying to provide custom genome to the pipeline, I’m getting the following error and I noticed that it is fixed when I unzip the fasta file.

Command used and terminal output

Error executing process > 'NFCORE_ATACSEQ:ATACSEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (null)'

Caused by:
  Not a valid path value type: groovyx.gpars.dataflow.DataflowVariable (DataflowVariable(value=null))

Relevant files

In the config file I’m using these in the params section: fasta = '/oak/stanford/groups/smontgom/kameronr/methylseq/JG97/genomes/GRCm39_fasta/GRCm39.genome.fa.gz' bwa_index = '/oak/stanford/groups/smontgom/kameronr/methylseq/JG97/genomes/GRCm39_fasta/'
gtf = '/oak/stanford/groups/smontgom/kameronr/methylseq/JG97/genomes/GRCm39_gtf/Mus_musculus.GRCm39.106.gtf' macs_gsize = 2728222451

System information

No response

sergpolly commented 1 year ago

exact same here. crashes with the error message above when fasta is compressed, proceeds beautifully when fasta is a text file ... Have to admit it wasn't easy to debug - as all of the work folders are empty and .nextflow.log isn't very informative in this case

JoseEspinosa commented 1 year ago

Should be fixed now in dev in case you want to give it a try.

JoseEspinosa commented 1 year ago

Will close this issue now, feel free to reopen it if you find any further issue.