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MMARINeDNA / metabarcoding_QAQC_pipeline

Pipeline scripts for initial quality control, ASV assignment, taxonomic classification, and preliminary data visualization
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Path errors: `scripts` #13

Closed invertdna closed 1 year ago

invertdna commented 1 year ago

I believe scripts has been replaced by bin, and so paths pointing at scripts are broken.

invertdna commented 1 year ago

still having this issue: sh: ../../bin/primer_trimming.sh: No such file or directory

Although I now think the setup script copies everything from bin in the main script folder into a scripts folder in the target working folder, and I'm not clear which version of the primer_trimming.sh the main metabarcoding_wrapper.sh is intending to call.

invertdna commented 1 year ago

for example, line 22 of metabarcoding_wrapper.sh has:

sh ../../bin/primer_trimming.sh

But at that point in the script, the working directory should be in {INPUT_DIR}/raw_fastqs, and there is no bin folder in the INPUT_DIR as created by the setup script.

alexandriai168 commented 1 year ago

fixed on config file, should be no more discrepancies between metabarcoding_wrapper.sh and config.sh