why not using the Samplesheet.csv in the inputdir? e.g /work/project/PlaGe/data/NovaSeq/240212_A00318_0475_BHWGKWDSX7_Lane1_1707895060/SampleSheet.csv this one is extracted from NGL, so the data is coherent and it would lower the number of NGL API calls
find the explanation. Extracting metadata file for raw read submission from ng6 and NGL for the same run/project to compare, we found a difference in md5sum.
seems we have the same md5sum in NGL, on server for NGL and NG6.....but differs in OCU_GRAAL_Run1.tsv.... @ckuchly can you check your workflow for OCU_GRAAL_Run1.tsv creation and md5sum affectation please
problem came from run selection for md5sum and comparison with NGL data (2 runs were done on the same libs https://ng6.toulouse.inra.fr/projects?tx_nG6_pi1%5Bproject_id%5D=2225&cHash=d3484aeb4632c192413d3b6b18d62050). If we work on the correct run, the md5 sums are identical
find the explanation. Extracting metadata file for raw read submission from ng6 and NGL for the same run/project to compare, we found a difference in md5sum.
seems we have the same md5sum in NGL, on server for NGL and NG6.....but differs in OCU_GRAAL_Run1.tsv.... @ckuchly can you check your workflow for OCU_GRAAL_Run1.tsv creation and md5sum affectation please
There is an endpoint in NGL-SQ to get the index object (in collection ngl_common.Parameter) GET /api/parameters/:typeCode/:code controllers.commons.api.Parameters.get(typeCode:java.lang.String,code:java.lang.String)
typeCode can be : index-illumina-sequencing | index-nanopore-sequencing | index-pacbio-sequencing
same locations on readsets as nanopore in fastq_rename.pl to get relevant information.....but, we need the index of barcode, not barcode name. we have to check how to get the sequence knowing the barcode name
currently, the names of fastq files on NGL are the default one, e.g. ECHSPCFR24fgt1234567_S60_L001_R2_001_filtered.fastq.gz on NG6 it is : ECHSPCFR24fgt1234567_GTGTAG-LHKP4_L001_R1.fastq.gz
to make easier (and possible) migration to NGL, the filenames must have the same name (so that we can access files from NG6 and NGL at the same time).
apply for illuina what is done with nanopore (get information from NGL for index and flowcell barcodes)
Bause of carbon footprint, it should be interesseting to use HitSat instead of STAR to align ARN reads.
Evaluation of this tool could be done in Mantis, before add it in the pipeline.
Need to trim :
Jules Sabban (abbb1ca8) at 22 Nov 11:35
Merge branch 'dev_Jules' into 'master'
Jules Sabban (4a670904) at 22 Nov 11:27
Merge branch 'dev_Jules' into 'master'
... and 10 more commits
The new path is available on both genologin and genobioinfo
The new path is available on both genologin and genobioinfo
Jules Sabban (09460954) at 17 Nov 16:42
Update bwa version in fastqscreen conf file
Only STAR outputs bam file
Jules Sabban (1b00ea8f) at 17 Nov 16:36
Run Qualimap for RNA data
Only STAR outputs bam file
Jules Sabban (944f0d1d) at 17 Nov 16:32
More memory for SORTMERNA and QUALIMAP
Error in field number to get GC_DROPOUT
value