mirTrace produces an error in test nextflex

[atrigila]

mirTrace cannot automatically detect the adapters and phred scores in nextflex data and therefore the pipeline fails. This is solved by using a configuration file. The nf-core module should allow using a configuration file.

Solution:

    def mirtrace_mode = mirtrace_config ? "--config ${mirtrace_config}": "${reads}"

    mirtrace qc  \\
        --species ${mirtrace_species} \\
        --write-fasta \\
        --output-dir . \\
        --force \\
        ${mirtrace_mode}

[lpantano]

question, is this happening even using the params.protocol=nextflex that will be used with mirtrace?

[atrigila]

yes, but it is because after adding the nextflex test a PR with nf-core mirtrace/qc was merged and the design did not allow for config files to be used (which we did in the original local module). The above PR should fix it :)