Verify LIMS data is valid for workflow processing

mskcc / hermes

Data collection management and analysis of information

Apache License 2.0

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Verify LIMS data is valid for workflow processing #7

Open aef- opened 4 years ago

aef- commented 4 years ago

Requires CMO ID

rhshah commented 4 years ago

Note: this is true only for the BAM generation workflow, for other workflow there will be more requirements. I can only think of CMO ID right now in BAM generation workflow, @ionox0 do you have any other field that we should check before launching the BAM generation workflow.

ionox0 commented 4 years ago

are we referring to the fastq_to_bam.cwl ?

if so here are all the required inputs that should come from LIMS:

adapter
adapter2
read_group_sample_name
read_group_sequencing_center
read_group_sequencing_platform
read_group_platform_unit
read_group_identifier
read_group_library
read_group_platform_unit

@aef- @rhshah

ionox0 commented 4 years ago

Actually, sorry again, I believe if we want the minimal inputs, then only these are strictly necessary:

"read_group_identifier": "test",
"read_group_library": 1,
"read_group_platform_unit": "IDT11",
"read_group_sample_name": "test",

as shown in the example inputs here:

https://app.gitbook.com/@msk-access/s/fastq-to-bam/inputs-description

aef- commented 4 years ago

Spoke with Sinisa -- this will be implemented in the Operator and a notification will be sent to Seqosystem when data is lacking.