Closed rifius closed 2 months ago
@matthdsm any thoughts? I'm wondering if it's the publishing and the naming of the sample with an _
that's the issue.
I think it's the sample naming that's the issue here. De demux modules glob on **[!Undetermined]_S*_R?_00?.fastq.gz
to find the output fastq's and the names with _R*
cause some kind of collision.
@rifius, could you post an ls
of the bclconvert
work dir so we can check out the filenames?
Other option now available: 10X mkfastq is now available on dev
and soon in 1.5.0 too
Description of the bug
I run the
bclconvert
demux on a 10x single cell and some fastq files are not copied / linked to the output folder, their md5sums not computed andfalco
,fastp
processes on them are not launched. In consequence, they are also missing from the QC reports.Setup:
bclcvt-sampleindex.csv
):[BCLConvert_Settings] CreateFastqForIndexReads,0
[BCLConvert_Data] Sample_ID,index CAM17_RoGr,ACGTCCCT CAM17_RoGr,CGCATGTG CAM17_RoGr,GAAGGAAC CAM17_RoGr,TTTCATGA CAM22_JoMc,AACCGTAA CAM22_JoMc,CTAAACGG CAM22_JoMc,GGTTTACT CAM22_JoMc,TCGGCGTC CAM27_ElBr,AACGTCAA ....
id,samplesheet,lane,flowcell A00999,/full/path/to/bclcvt-sampleindex.csv,,/full/bcl/data/path
Relevant files
nf.log.gz
System information
Version: 23.04.1 build 5866 Created: 15-04-2023 06:51 UTC (16:51 AEDT) System: Linux 6.3.12-200.fc38.x86_64 Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 17.0.6+10 Encoding: UTF-8 (UTF-8) Process: 2401714@my-machine [10.x.x.x] CPUs: 32 - Mem: 503.3 GB (6.2 GB) - Swap: 0 (0)
nf-core/demultiplex v1.3.2-g67b8465
Container engine: podman rootless OS: Fedora Core OS