For whatever reason, the current version of FastQC treats .fastq and .fq files differently. The subfolder for datafile_0.fastq is datafile_0_fastqc, while for datafile_0.fq it's datafile_0.fq_fastqc. Thus .fq files fail in project.paired_WGseq.install_3.sh:244, since the subfolder FASTQC_temp_file doesn't exist - we can't simply replace the extension with _fastqc, as we do on line 239. Probably we should try finding the subfolder (there are only two entries in the FastQC folder, one is a zip file and the other is the subfolder of interest) regardless of its name, perhaps by taking the name that doesn't end with .zip.
For whatever reason, the current version of FastQC treats
.fastqand.fqfiles differently. The subfolder fordatafile_0.fastqisdatafile_0_fastqc, while fordatafile_0.fqit'sdatafile_0.fq_fastqc. Thus.fqfiles fail inproject.paired_WGseq.install_3.sh:244, since the subfolderFASTQC_temp_filedoesn't exist - we can't simply replace the extension with_fastqc, as we do on line 239. Probably we should try finding the subfolder (there are only two entries in the FastQC folder, one is a zip file and the other is the subfolder of interest) regardless of its name, perhaps by taking the name that doesn't end with.zip.