Meet template convention #21
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| params { | |||
| igenomes_base = 's3://ngi-igenomes/igenomes' | |||
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I think we had agreed that all this was supposed to point to either the eu-west1 featured bucked or the original featured bucket, if I remember correctly. Do we still need to keep the igenome??
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| params { | |||
| igenomes_base = 's3://ngi-igenomes/igenomes' | |||
| reference_bucket = 's3://lifebit-featured-datasets/' | |||
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| reference_bucket = 's3://lifebit-featured-datasets/' | |
| reference_data_bucket = 's3://lifebit-featured-datasets/' |
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| params { | |||
| igenomes_base = 's3://reference-data-cyn-pro/igenomes' | |||
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| igenomes_base = 's3://reference-data-cyn-pro/igenomes' | |
| reference_data_bucket = 's3://reference-data-cyn-pro/igenomes' |
if we need to keep this for cynapxe, then maybe it would be best to have it as reference_data_bucket
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| docker.enabled = true | |||
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| params { | |||
| input = "testdata/input_mix_vcf_origin.tsv" | |||
| input = "s3://lifebit-featured-datasets/pipelines/mutational-signature-nf/testdata/input_mix_vcf_origin.tsv" | |||
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| input = "s3://lifebit-featured-datasets/pipelines/mutational-signature-nf/testdata/input_mix_vcf_origin.tsv" | |
| input = "${params.reference_data_bucket}"/pipelines/mutational-signature-nf/testdata/input_mix_vcf_origin.tsv" |
| @@ -92,6 +103,9 @@ profiles { | |||
| cloudos_production_test_2 { includeConfig 'conf/cloudos_production_test_2.config' } | |||
| } | |||
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| includeConfig 'conf/containers/quay.config' | |||
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this line has to go before the profile definition otherwise it will not work on ihis and it's already there, so I would remove it from here!
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there are no reference files for this pipeline?
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also here https://github.com/lifebit-ai/mutational-signature-nf/blob/74e1bebcf78d67bcc1755359a8085da01197d65b/nextflow.config#L37C5-L37C49 there's this container definition that is not parametrised. I am not sure that this is ever used but we might need to double check that!
| signature_tool_lib_container = "518054667335.dkr.ecr.${params.container_region}.amazonaws.com/lifebitai/signature_tool_lib:1e58326" | ||
| utility_scripts_container = "518054667335.dkr.ecr.${params.container_region}.amazonaws.com/lifebitai/utility_scripts:b586275" | ||
| awscli_bcftools_container = "518054667335.dkr.ecr.${params.container_region}.amazonaws.com/lifebitaiorg/awscli_bcftools_comb:v0.1" | ||
| main_container = '518054667335.dkr.ecr.${params.container_region}.amazonaws.com/lifebitai/ubuntu:18.10' |
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These all need the double quotes, otherwise the ${params.container_region} will not be compiled and it will be used as a string.
Overview
Purpose
To have curated pipeline in IHIS.
Acceptance Criteria/Jira Ticket
DEL-15019
Changes
Internal CloudOS Tests
Client CloudOS Tests
PR Checklist
Author to check:
[Fix:|Feat:|Docs:]based on PR typedevbranch for DSL1 orDSL2-devfor DSL2 translations