It was found that stringti_merged results folder as well as some other folders are missing all or some files. Most probably that started happening after output pattern update needed to save .command.* logs in #251 .
This PR fixes the issues.
To test:
git clone https://github.com/TheJacksonLaboratory/splicing-pipelines-nf
cd splicing-pipelines-nf
git fix-saving-files
NXF_VER=20.01.0 nextflow run . -profile ultra_quick_test,docker --test false
The job will fail on the last process, but that's expected.
Then check folders:
results/star_mapped/count_matrix for sample_lst.txt file;
results/star_mapped/stringtie_merge for all files (all were missing before);
Vlad-Dembrovskyi
commented
2 years ago
It was found that stringti_merged results folder as well as some other folders are missing all or some files. Most probably that started happening after output pattern update needed to save .command.* logs in #251 .
This PR fixes the issues.
To test:
The job will fail on the last process, but that's expected.
Then check folders:
results/star_mapped/count_matrixforsample_lst.txtfile;results/star_mapped/stringtie_mergefor all files (all were missing before);results/MultiQCformultiqc_datafolder.