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sidbdri / cookiecutter-de_analysis_skeleton

Skeleton for new differential expression analysis project.
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incorrect passing fastq files due to READ1/2_IDENTIFIER setting in paired-end/single-end data #211

Closed hxin closed 1 year ago

hxin commented 1 year ago

https://github.com/sidbdri/cookiecutter-de_analysis_skeleton/blob/3ff1fbc8cb9d02c69ac5a6d9ec91395c54615bcc/%7B%7Bcookiecutter.project_name%7D%7D/snake_variables.py#L63

https://github.com/sidbdri/cookiecutter-de_analysis_skeleton/blob/45097618cb7623f220fe226fa53563683d64bada/%7B%7Bcookiecutter.project_name%7D%7D/Snakefile.singlespecies_analysis#L27

In the case of single-end reads, ‘*’ is passed to the function, which will incorrectly pass all fastq.gz file as read1 AND read2 reads.