search

fls-bioinformatics-core / auto_process_ngs

Scripts and utilities for automatic processing & management of Illumina NGS sequencing data.
Other
9 stars 6 forks source link

'make_fastqs': put processing outputs and stats into a single 'processing' subdirectory #932

Open pjbriggs opened 6 months ago

pjbriggs commented 6 months ago

Proposal to put all the statistics and other processing outputs from the make_fastqs command into a single processing subdirectory, to make the top level of the analysis directory tidier.

For example currently it might look like:

auto_process.info
barcode_analysis
bcl2fastq/
custom_SampleSheet.csv
logs/
metadata.info
per_lane_sample_stats.info
per_lane_statistics.info
primary_data/
processing_qc.html
projects.info
SampleSheet.orig.csv
ScriptCode/
statistics_full.info
statistics.info

but instead we could have e.g.

auto_process.info
bcl2fastq/
custom_SampleSheet.csv
logs/
metadata.info
primary_data/
processing/
projects.info
SampleSheet.orig.csv
ScriptCode/

with the QC report, stats files and barcodes all under the processing subdir. (This might also simplify things when using the --id option for the make_fastqs command, as the processing subdir could also have the appropriate ID appended.)