Clinical-Genomics / microSALT

Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.
GNU General Public License v3.0
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Make validation samples available #144

Closed talnor closed 1 year ago

talnor commented 2 years ago

Describe the bug The following projects are used to validate microSALT: MIC3109, MIC4107, MIC4109 & ACC5551.

Expected behavior All cases and samples should be available for validations in cg.

Additional context

Updating compress api Set dry run to False Fetch latest version from bundle ACC5551A31 Found file /home/proj/production/demultiplexed-runs/190417_A00621_0064_AHJM7JDSXX/Unaligned-Y151I10I10Y151/Project_609108/Sample_ACC5551A31/HJM7JDSXX_609108_S313_L004.spring Found file /home/proj/production/demultiplexed-runs/190417_A00621_0064_AHJM7JDSXX/Unaligned-Y151I10I10Y151/Project_609108/Sample_ACC5551A31/HJM7JDSXX_609108_S313_L002.spring Found file /home/proj/production/demultiplexed-runs/190417_A00621_0064_AHJM7JDSXX/Unaligned-Y151I10I10Y151/Project_609108/Sample_ACC5551A31/HJM7JDSXX_609108_S313_L001.spring Found file /home/proj/production/demultiplexed-runs/190417_A00621_0064_AHJM7JDSXX/Unaligned-Y151I10I10Y151/Project_609108/Sample_ACC5551A31/HJM7JDSXX_609108_S313_L003.spring Check if pending compression file exists /home/proj/production/demultiplexed-runs/190417_A00621_0064_AHJM7JDSXX/Unaligned-Y151I10I10Y151/Project_609108/Sample_ACC5551A31/HJM7JDSXX_609108_S313_L004.crunchy.pending.txt does not exist Check if SPRING archive file exists Check if FASTQ pair exists FASTQ files already exists SPRING to FASTQ decompression not possible for ACC5551A31 Skipping sample ACC5551A31

pbiology commented 1 year ago

Will be part of validation strategy in JASEN. Clinical-Genomics/CG-JASEN#3