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Wrong BWA index directory in references #70
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It seems that BWA index directory and the directory to which the travis.yml refers to don't match. I've tried changing the directory of BWA index files, and it was of no help. My local BWA index directory is: /home/lab32/references/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/ The pipeline creates a folder like this: /home/lab32/Downloads/teste/results/reference_genome/BWAIndex/BWAIndex However, travis.yml refers to this: /home/lab32/Downloads/teste/results/reference_genome/BWAIndex/ P.S: I downloaded those files from AWS IGenome. They have already been tested with the standalone version of CIRIquant and it worked. |
Hey @Lupezes, I'm in the process of switching to DSL2, can I ask you to use the dev branch? Your command would be: nextflow pull -r dev nf-core/circrna nextflow run -r dev nf-core/circrna \
-profile docker \
--input test_samples.csv \
--genome GRCh38 \
--module 'circrna_discovery,mirna_prediction' \
--tool 'ciriquant' \
--bwa "/home/lab32/references/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/" \
--gtf "/home/lab32/references/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" \
--mature "/home/lab32/references/Homo_sapiens/NCBI/GRCh38/Annotation/SmallRNA/mature.fa" You shouldn't need bowtie, bowtie2 nor STAR for CIRIquant. Pass the hisat2 reference if you have it in your directory! We don't make use of the reference bed12 file either. I'll hold off on committing to dev for the evening so you get a chance to run it. Best, Barry |
Hi @BarryDigby! I was using a previous version, because I wasn't able to make the current one work properly!
Here is is the nextflow workflow report
execution_report_2023-01-31_15-47-19.zip Just to ensure the files are in the correct directory:
I believe this is a problem to be solved in another issue, however I could make the 'test' profile of this version work. |
Ah, you did not surround your BWAIndex path with quotes ;) edit: does not appear to solve it, leave it with me an I will sort it out this morning |
Going to document the cause here for my future self:
CIRIQUANT_YML( gtf, fasta, bwa_index.map{ meta, index -> return index }, hisat2_index ) BWA indices are output as a bwa_index = params.fasta ? params.bwa ? Channel.fromPath(params.bwa).map{ it -> [[id:it[0].baseName], it] } : PREPARE_GENOME.out.bwa : [] Check PREPARE_GENOME outputsBowtie/data/github/circrna/work/fb/e5d28f3ff1cd6938ab26ee490c0297/bowtie Bowtie2[[id:chrI], /data/github/circrna/work/a3/72d197d22a067c5461fb4a51e71152/bowtie2] BWA[[id:chrI], /data/github/circrna/work/61/6c66997160f35498e68d457a318585/bwa] HISAT2/data/github/circrna/work/b0/4d79b66f3622747dcde57d4fa4f716/hisat2 STAR/data/github/circrna/work/20/e64c9b4a063dae0ed545b0c24ddd7a/star Segemehl/data/github/circrna/work/92/828329416bcb2eb29efeb9fb5278aa/chrI.idx Make sure to make a tuple when user supplies path to |
@Lupezes Thanks for raising the issue - good catch. Just double checking everything now on the dev branch. If you're able to hang tight the dev branch should be released as version 1.0.0 later this week |
@BarryDigby Thank you for the attention! No problem! I'll be waiting for the release then. |
Description of the bug
CIRIquant step can't find BWA index files.
This behaviour is seen regardless if reference files are fetched from AWS or locally assigned.
Command used and terminal output
Relevant files
nextflow.log
System information
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