Require: Support multiple fastq files in subfolder. #36
Description
Falco version 1.0.0 could not parse the correct output directory, when I work on multiple fastq files within subfolder.
Here is the directory structure:
$ tree demo/
demo/
├── test_rep1.fq.gz
└── test_rep2.fq.gz
Then Run Falco as following:
$ falco demo/*gz
[limits] using default limit cutoffs (no file specified)
[adapters] using default adapters (no file specified)
[contaminants] using default contaminant list (no file specified)
[Fri Sep 2 08:46:59 2022] Started reading file demo/test_rep1.fq.gz
[Fri Sep 2 08:46:59 2022] reading file as gzipped FASTQ format
[running falco|===================================================|100%]
[Fri Sep 2 08:46:59 2022] Finished reading file
[Fri Sep 2 08:46:59 2022] Writing text report to demo/demo/test_rep1.fq.gz_fastqc_data.txt
[Fri Sep 2 08:46:59 2022] Writing HTML report to demo/demo/test_rep1.fq.gz_fastqc_report.html
Elapsed time for file demo/test_rep1.fq.gz: 0s
[limits] using default limit cutoffs (no file specified)
[adapters] using default adapters (no file specified)
[contaminants] using default contaminant list (no file specified)
[Fri Sep 2 08:46:59 2022] Started reading file demo/test_rep2.fq.gz
[Fri Sep 2 08:46:59 2022] reading file as gzipped FASTQ format
[running falco|===================================================|100%]
[Fri Sep 2 08:46:59 2022] Finished reading file
[Fri Sep 2 08:46:59 2022] Writing text report to demo/demo/test_rep2.fq.gz_fastqc_data.txt
[Fri Sep 2 08:46:59 2022] Writing HTML report to demo/demo/test_rep2.fq.gz_fastqc_report.html
Elapsed time for file demo/test_rep2.fq.gz: 0s
$ falco --version
falco 1.0.0
The subfolder path is duplicated as follow: (so could not generate output files)
Writing text report to demo/demo/test_rep1.fq.gz_fastqc_data.txt，