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dekkerlab / cLIMS-docker

cLIMS repository running on Docker Contaienrs
GNU Lesser General Public License v3.0
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example of clims ingest for nanopore data #95

Open sergpolly opened 1 year ago

sergpolly commented 1 year ago 
exp-name,path,type,runname,md5sum
b10,/pi/job.dekker-umw/cshare/nanopore/Liyan/20221215/20221215_5stages/20221215_lib1/20221215_1658_X1_FAV63654_90ce7081/fast5_fail/barcode10/FAV63654_fail_barcode10_90ce7081_597b19ca*,fastq,Liyan_20221215_5stages,123
b10,/pi/job.dekker-umw/cshare/nanopore/Liyan/20221215/20221215_5stages/20221215_lib1/20221215_1658_X1_FAV63654_90ce7081/fastq_fail/barcode10/FAV63654_fail_barcode10_90ce7081_597b19ca*,fast5,Liyan_20221215_5stages,234
b10,/pi/job.dekker-umw/cshare/nanopore/Liyan/20221215/20221215_5stages/20221215_lib1/20221215_1658_X1_FAV63654_90ce7081/fast5_pass/barcode10/FAV63654_pass_barcode10_90ce7081_597b19ca*,fastq,Liyan_20221215_5stages,345
b10,/pi/job.dekker-umw/cshare/nanopore/Liyan/20221215/20221215_5stages/20221215_lib1/20221215_1658_X1_FAV63654_90ce7081/fastq_pass/barcode10/FAV63654_pass_barcode10_90ce7081_597b19ca*,fast5,Liyan_20221215_5stages,987
b09,/pi/job.dekker-umw/cshare/nanopore/Liyan/20221215/20221215_5stages/20221215_lib1/20221215_1658_X1_FAV63654_90ce7081/fast5_fail/barcode09/FAV63654_fail_barcode09_90ce7081_597b19ca*,fastq,Liyan_20221215_5stages,444
b09,/pi/job.dekker-umw/cshare/nanopore/Liyan/20221215/20221215_5stages/20221215_lib1/20221215_1658_X1_FAV63654_90ce7081/fastq_fail/barcode09/FAV63654_fail_barcode09_90ce7081_597b19ca*,fast5,Liyan_20221215_5stages,898
b09,/pi/job.dekker-umw/cshare/nanopore/Liyan/20221215/20221215_5stages/20221215_lib1/20221215_1658_X1_FAV63654_90ce7081/fast5_pass/barcode09/FAV63654_pass_barcode09_90ce7081_597b19ca*,fastq,Liyan_20221215_5stages,100
b09,/pi/job.dekker-umw/cshare/nanopore/Liyan/20221215/20221215_5stages/20221215_lib1/20221215_1658_X1_FAV63654_90ce7081/fastq_pass/barcode09/FAV63654_pass_barcode09_90ce7081_597b19ca*,fast5,Liyan_20221215_5stages,104

this is with the 2 barcodes in that seq. run...

and now an example with no barcoding:

exp-name,path,type,runname,md5sum
wt,/pi/job.dekker-umw/cshare/nanopore/Nicola/MC3C_RPE1_minusBRDU/220307_MC3C_RPE1_minusBRDU/20220307_1729_MN18258_FAS56708_57dc419d/fast5_fail/FAS56708_fail_5ec70280*,fastq,Nicola_220307_MC3C_RPE1,555
wt,/pi/job.dekker-umw/cshare/nanopore/Nicola/MC3C_RPE1_minusBRDU/220307_MC3C_RPE1_minusBRDU/20220307_1729_MN18258_FAS56708_57dc419d/fastq_fail/FAS56708_fail_5ec70280*,fast5,Nicola_220307_MC3C_RPE1,666
wt,/pi/job.dekker-umw/cshare/nanopore/Nicola/MC3C_RPE1_minusBRDU/220307_MC3C_RPE1_minusBRDU/20220307_1729_MN18258_FAS56708_57dc419d/fast5_pass/FAS56708_pass_5ec70280*,fastq,Nicola_220307_MC3C_RPE1,777
wt,/pi/job.dekker-umw/cshare/nanopore/Nicola/MC3C_RPE1_minusBRDU/220307_MC3C_RPE1_minusBRDU/20220307_1729_MN18258_FAS56708_57dc419d/fastq_pass/FAS56708_pass_5ec70280*,fast5,Nicola_220307_MC3C_RPE1,888

let's see if we can use something like that as a cLIMS upload for cLIMS

should also generate some example uploads without fastq or without fast5 - I think both situations are potentially possible ...

Also seq. summary file to be added somehow

Snehal1894 commented 1 year ago
  1. Name- name_*.fastq.gz/fastq (will be added in the clims upload file)
  2. Add columns optional - sha256 and backup path
  3. "Type" column needed- for simplicity
  4. Paired End -1, Paired File-None (for Nanopore)

To use same import seq files button and filter the process using the sequencing platform (right now "Nanopore) Change Sequencing File model - add Metadata text field.