Add option to specify file output names

[moldach]

In cases where you have you have paired-end reads (e.g. HG03583_S1_L001_R1.fastq.gz & HG03583_S1_L001_R2.fastq.gz) or a number of FASTQ files in a directory falco will over-write fastqc_data.txt, fastqc_report.html and summary.txt.

At the moment the only way around this, I see, would be to have each FASTQ file in it's own directory (not ideal IMO).

It would be nice to be able to specify the name of output so you could use wild-card rules in a Snakemake workflow for example.

[guilhermesena1]

Hi Matthew,

You can make a custom output directory for fastq files using the -o argument. In your case, one possibility would be to run the following in the directory with the two end reads:

for i in R1 R2; do falco -o HG03583_S1_L001_${i} HG03583_S1_L001_${i}.fastq.gz; done

Which would create two directories, HG03583_S1_L001_R1 and HG03583_S1_L001_R2, with the respective data, summary and reports for each end of the read.

We chose to do it this way mostly because it's how FastQC does it, but we will add custom output filename options on the next release. I personally agree that users should have the freedom to choose the filename of every output.

[moldach]

Thanks for the suggestion @guilhermesena1

another idea

MuliQC can collect reports from FastQC's .zip output making it easier to compare results. Structuring the output of falco to emulate that of FastQC would allow this tool to work seamlessly with other tools that use the output from FastQC.

[guilhermesena1]

Hi Matthew,

Thank you for the suggestion. I believe that indeed if you zip the output files from falco, you should be able to run the output through MultiQC by "pretending" it comes from FastQC since the outputs should be identical. My memory is a bit fuzzy on it but it also might be possible that you only need the "fastqc_data.txt" file to generate multiqc reports, or that you can pass the directory generated by falco and MultiQC will look for the output files within it. I'd be very interested in knowing if MultiQC fails to parse your output files, and what error reports they generate in case you tried this.

[moldach]

Yes I'm in the process of `rolling my own` right now. It's nice when the tool does the work for me 🤷 But on a more serious note when you provide similar output it prevents every user from writing a custom _in-house_ solution FWIW

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On Sun., May 3, 2020, 16:31 Guilherme Sena, ***@***.***> wrote: Hi Matthew, Thank you for the suggestion. I believe that indeed if you zip the output files from falco, you should be able to run the output through MultiQC by "pretending" it comes from FastQC since the outputs should be identical. My memory is a bit fuzzy on it but it also might be possible that you only need the "fastqc_data.txt" file to generate multiqc reports, or that you can pass the directory generated by falco and MultiQC will look for the output files within it. I'd be very interested in knowing if MultiQC fails to parse your output files, and what error reports they generate in case you tried this. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABL3VWJ64TL35MMQTUTS2WLRPXWEXANCNFSM4MPR4NWA> .

[guilhermesena1]

only took me over 2 years but I finally got around to implementing this. Custom flags for the summary, report and data filenames (although only for single-input files). Done on commit 159e7f3