Closed sklages closed 3 years ago
Hello,
I assume you ran falco on several FASTQ files, which prepends the FASTQ name with an underscore(in this case sample_S17_L002_R1_001.fastq.gz_
) to the file names.
I believe MultiQC takes a directory as input and it looks for files named summary.txt
, fastqc_data.txt
and fastqc_report.html
exactly (without the prefix), so if you move these files to a directory (e.g. named the same as your FASTQ sample) and rename the 3 files to remove the prefix, it should work. Please let me know though if you still have trouble or if that solves the problem.
Hi,
I am running falco
on individual fastq files (for better logging/timestamping) and rename the standard files according to my sample names.
Yes, seems it takes a directory or zip file to search for content.
Now I changed my pipeline in that, that a correct subdir is created containing the relevant files, like:
|--sample_S17_L002_R1_001_fastqc
| |-- fastqc_data.txt
| |-- fastqc_report.html
| `-- summary.txt
`-- sample_S17_L002_R1_001_fastqc_report.html -> sample_S17_L002_R1_001_fastqc/fastqc_report.html
together with a symlink (properly named for user convenience) pointing to fastqc_report.html
.
Well, it works :-)
Testing on a small 4GB fastq file shows, that falco
runs 2-2.5x faster compared to fastqc
(single-threaded). Running fastqc
with 4 threads on a single fastq file, is not faster than single-threaded (as expected). Running fastqc
with 4 threads on a pair of fastq files, it runs the same time as for one file, nowusing 2 cores.
So I think I will stick with falco
for now, although the HTML report is not yet "perfect" (e.g. some tables do not match the page/report design).
Thanks for a nice piece of software!
As I understood, current version
0.2.4
output should be compatible with currentmultiqc
, I am using1.9
.No matter which files I create with
falco
,multiqc
always fails to find any analysis results.Even when putting these files into
sample_S17_L002_R1_001.fastq.gz.zip
... no success.So I obviously missed here soemthing probably very basic/simple.
Any idea what I am doing wrong?