CIRIquant test fails since commit 72dd514, PR #104

[MariekeVromman]

Description of the bug

I'm running into a ciriquant error since #104, specifically after this commit 72dd514.

Reproducible by checking out that commit and running the test data git checkout 72dd514cc90d19797bf3869b9427d879677582f6 nextflow run circrna -profile test,docker,arm --tool ciriquant

Error: Traceback (most recent call last): File "/usr/local/bin/CIRIquant", line 10, in <module> sys.exit(main()) File "/usr/local/lib/python2.7/site-packages/CIRIquant/main.py", line 89, in main config = check_config(check_file(args.config_file)) File "/usr/local/lib/python2.7/site-packages/CIRIquant/utils.py", line 107, in check_config raise ConfigError('Could not find hisat2 index with suffix: *.[1-8].ht2 or *.[1-8].ht2l, please check your configuration') CIRIquant.utils.ConfigError: Could not find hisat2 index with suffix: *.[1-8].ht2 or *.[1-8].ht2l, please check your configuration

When reverting back to commit c4a3e8e (one commit earlier), this error does not occur, and the CIRCRNA_DISCOVERY:CIRIQUANT processes end successfully. (Another error occurs later in the pipeline but I think this is not important here.)

@nictru , tagging you as you might have a better understanding of the changes :)

Command used and terminal output

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Relevant files

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System information

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[MariekeVromman]

I tried to look a bit closer at this bug. It's a bit annoying to reproduce as there are multiple bugs (some of which are already resolved in the newer version of the pipeline). But I think it comes down to this:

Before commit 72dd514, the creation of the yaml file included this

in script: hisat2_prefix = fasta.toString() - ~/.(fa|fasta)$/

and then further printf "name: ciriquant\ntools:\n bwa: \$BWA\n hisat2: \$HISAT2\n stringtie: \$STRINGTIE\n samtools: \$SAMTOOLS\n\nreference:\n fasta: ${fasta_path}\n gtf: ${gtf_path}\n bwa_index: ${bwa_path}/\$BWA_FILE\n hisat_index: ${hisat2_path}/${hisat2_prefix}" >> travis.yml

when looking at the created file travis.yml:

hisat_index: /Users/marieke/Documents/ciriquant/work/e4/16de17aae2f6a3e21f4454b48a54bb/hisat2/chrI

However, with the commit commit 72dd514, line 22 in this script changed to

hisat2_prefix = meta2.id taking form the input tuple val(meta2), path(fasta) where meta2 just contains the word fasta and therefore the travis.yml file then contains:

hisat_index: /Users/marieke/Documents/ciriquant/work/e8/aebdbd37ab6875b8dfa62c0e7e9d4b/hisat2/fasta

Which is I think the cause of the error mentioned above

[nictru]

Looks plausible, we should revert the change in line 22 in this case - thanks for pointing this out

[MariekeVromman]

ah yes, I'm just doing the PR right now :)