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feat: separate entities into seqerakit yamls
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compute-envs: | ||
- name: "seqera_aws_ireland_dragen" | ||
workspace: "seqeralabs/showcase" | ||
credentials: "seqera_aws_management_credentials" | ||
wait: "AVAILABLE" | ||
file-path: "../compute-envs/seqera_aws_ireland_dragen.json" | ||
overwrite: False |
22 changes: 22 additions & 0 deletions
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seqerakit/compute-envs/seqera_aws_ireland_fusionv2_nvme.yml
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compute-envs: | ||
- type: aws-batch forge | ||
name: "seqera_aws_ireland_fusionv2_nvme" | ||
workspace: "seqeralabs/showcase" | ||
credentials: "seqera_aws_development_credentials" | ||
region: "eu-west-1" | ||
work-dir: "s3://seqeralabs-showcase" | ||
wave: True | ||
fusion-v2: True | ||
fast-storage: true | ||
provisioning-model: "SPOT" | ||
instance-type: "c6id,m6id,r6id" | ||
max-cpus: 500 | ||
allow-buckets: | ||
[ | ||
"s3://ngi-igenomes", | ||
"s3://nf-core-awsmegatests", | ||
"s3://seqeralabs-showcase", | ||
] | ||
head-job-role: "$HEAD_JOB_IAM_ROLE" | ||
wait: "AVAILABLE" | ||
overwrite: False |
21 changes: 21 additions & 0 deletions
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seqerakit/compute-envs/seqera_aws_ireland_fusionv2_nvme_gpu.yml
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compute-envs: | ||
- type: aws-batch forge | ||
name: "seqera_aws_ireland_fusionv2_nvme_gpu" | ||
workspace: "seqeralabs/showcase" | ||
credentials: "seqera_aws_development_credentials" | ||
region: "eu-west-1" | ||
work-dir: "s3://seqeralabs-showcase" | ||
wave: True | ||
fusion-v2: True | ||
fast-storage: true | ||
provisioning-model: "SPOT" | ||
instance-type: "g4dn" | ||
max-cpus: 500 | ||
allow-buckets: | ||
[ | ||
"s3://ngi-igenomes", | ||
"s3://nf-core-awsmegatests", | ||
"s3://seqeralabs-showcase", | ||
] | ||
wait: "AVAILABLE" | ||
overwrite: False |
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compute-envs: | ||
- type: aws-batch forge | ||
name: "seqera_aws_ireland_s3" | ||
workspace: "seqeralabs/showcase" | ||
credentials: "seqera_aws_development_credentials" | ||
region: "eu-west-1" | ||
work-dir: "s3://seqeralabs-showcase" | ||
provisioning-model: "SPOT" | ||
max-cpus: 500 | ||
allow-buckets: | ||
[ | ||
"s3://ngi-igenomes", | ||
"s3://nf-core-awsmegatests", | ||
"s3://seqeralabs-showcase", | ||
] | ||
cli-path: "/home/ec2-user/miniconda/bin/aws" | ||
wait: "AVAILABLE" | ||
overwrite: False |
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compute-envs: | ||
- type: azure-batch forge | ||
name: "seqera_azure_virginia_fusion" | ||
workspace: "seqeralabs/showcase" | ||
credentials: "seqera_azure_development_credentials" | ||
location: "eastus" | ||
work-dir: "az://azure-benchmarking" | ||
fusion-v2: True | ||
wave: True | ||
vm-count: 1 | ||
vm-type: "Standard_E16d_v5" | ||
registry-credentials: seqera_dockerhub_credentials |
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compute-envs: | ||
- type: google-batch | ||
name: "seqera_gcp_finland_fusion" | ||
workspace: "seqeralabs/showcase" | ||
credentials: "seqera_gcp_credentials" | ||
location: "europe-north1" | ||
work-dir: "gs://seqeralabs-showcase-eu-north-1" | ||
fusion-v2: True | ||
wave: True | ||
spot: True | ||
boot-disk-dize: 200 | ||
wait: "AVAILABLE" | ||
overwrite: False |
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compute-envs: | ||
- type: slurm | ||
name: "seqera_slurm" | ||
workspace: "seqeralabs/showcase" | ||
credentials: "seqera_slurm_credentials" | ||
work-dir: "/home/ubuntu/work" | ||
launch-dir: "/home/ubuntu/showcase-launchdir" | ||
user-name: "ubuntu" | ||
host-name: "slurm.seqera.io" | ||
head-queue: "long" | ||
compute-queue: "long" | ||
wait: "AVAILABLE" | ||
overwrite: False |
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datasets: | ||
- name: "SRP459762-carcinoma-sra-ids" | ||
description: 'Immunological subtyping of salivary gland cancer identifies histological origin-specific tumor immune microenvironment SRA: SRP459762\nBioProject: PRJNA1014965' | ||
header: True | ||
workspace: "seqerakit-e2e/showcase" | ||
file-path: "../../datasets/SRP459762-carcinoma-sra-ids.csv" | ||
overwrite: False |
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datasets: | ||
- name: "proteinfold_sequences" | ||
description: "Samplesheet containing links to fasta files required to test the nf-core/proteinfold pipeline from end-to-end." | ||
header: True | ||
workspace: "seqerakit-e2e/showcase" | ||
file-path: "../../datasets/proteinfold_sequences.csv" | ||
overwrite: False |
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datasets: | ||
- name: "SRP459762-carcinoma-samplesheet" | ||
description: 'Samplesheet containing SRA IDs required to test the nf-core/rnaseq pipeline (v3.10) from end-to-end.\nFurther information about how the dataset was created can be obtained via the link below:\nhttps://github.com/nf-core/test-datasets/tree/rnaseq#minimal-test-dataset-origin' | ||
header: True | ||
workspace: "seqerakit-e2e/showcase" | ||
file-path: "../../datasets/SRP459762-carcinoma-samplesheet.csv" | ||
overwrite: False |
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datasets: | ||
- name: "rnaseq_samples" | ||
description: 'Samplesheet containing links to minimal data required to test the nf-core/rnaseq pipeline (v3.10) from end-to-end.\nFurther information about how the dataset was created can be obtained via the link below:\nhttps://github.com/nf-core/test-datasets/tree/rnaseq#minimal-test-dataset-origin' | ||
header: True | ||
workspace: "seqerakit-e2e/showcase" | ||
file-path: "../../datasets/rnaseq_samples.csv" | ||
overwrite: False |
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datasets: | ||
- name: "sarek_samples" | ||
description: "Samplesheet containing links to minimal data required to test the nf-core/sarek pipeline (v3.1.2) from end-to-end." | ||
header: True | ||
workspace: "seqerakit-e2e/showcase" | ||
file-path: "../../datasets/sarek_samples.csv" | ||
overwrite: False |
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datasets: | ||
- name: "viralrecon_illumina_samples" | ||
description: 'Samplesheet containing links to minimal Illumina data required to test the nf-core/viralrecon pipeline (v2.5) from end-to-end.\nFurther information about how the dataset was created can be obtained via the link below:\nhttps://github.com/nf-core/test-datasets/tree/viralrecon#content-of-this-repository' | ||
header: True | ||
workspace: "seqerakit-e2e/showcase" | ||
file-path: "../../datasets/viralrecon_illumina_samples.csv" | ||
overwrite: False | ||
- name: "viralrecon_nanopore_samples" | ||
description: "Samplesheet containing links to minimal Nanopore metadata required to test the nf-core/viralrecon pipeline (v2.5) from end-to-end." | ||
header: True | ||
workspace: "seqerakit-e2e/showcase" | ||
file-path: "../../datasets/viralrecon_nanopore_samples.csv" | ||
overwrite: False |
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datasets: | ||
- name: "dragen_samples" | ||
description: "Samplesheet containing links to minimal data required to test the seqeralabs/nf-dragen pipeline from end-to-end" | ||
header: True | ||
workspace: "seqerakit-e2e/showcase" | ||
file-path: "../../datasets/dragen_samples.csv" | ||
overwrite: False |
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datasets: | ||
- name: "sentieon_samples" | ||
description: "Samplesheet containing links to minimal data required to test the seqeralabs/nf-sentieon pipeline from end-to-end" | ||
header: True | ||
workspace: "seqerakit-e2e/showcase" | ||
file-path: "../../datasets/sentieon_samples.csv" | ||
overwrite: False |
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pipelines: | ||
- name: "hello" | ||
description: "Classic hello world script in Nextflow language" | ||
url: "https://github.com/nextflow-io/hello" | ||
compute-env: "seqera_aws_ireland_fusionv2_nvme" | ||
revision: "master" | ||
labels: "hello-world" | ||
pre-run: "./pre-run.sh" | ||
overwrite: False |
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pipelines: | ||
- name: "nf-core-fetchngs" | ||
description: "Pipeline to fetch metadata and raw FastQ files from public and private databases" | ||
url: "https://github.com/nf-core/fetchngs" | ||
workspace: "seqeralabs/showcase" | ||
compute-envs: "seqera_aws_ireland_fusionv2_nvme" | ||
revision: "1.10.1" | ||
profile: "test" | ||
labels: ["download", "ena", "sra"] | ||
pre-run: "./pre-run.sh" | ||
params: | ||
outdir: "s3://seqeralabs-showcase/nf-core-fetchngs/results" | ||
force_sratools_download: True | ||
nf_core_pipeline: "rnaseq" | ||
overwrite: False |
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outdir: "s3://seqeralabs-showcase/nf-core-proteinfold/results" | ||
use_gpu: true | ||
alphafold2_db: "s3://ngi-igenomes/test-data/proteinfold/db/alphafold_mini" | ||
bfd_path: "s3://ngi-igenomes/test-data/proteinfold/db/alphafold_mini/bfd/*" | ||
small_bfd_path: "s3://ngi-igenomes/test-data/proteinfold/db/alphafold_mini/small_bfd/*" | ||
alphafold2_params_path: "s3://ngi-igenomes/test-data/proteinfold/db/alphafold_mini/alphafold_params_*/*" | ||
mgnify_path: "s3://ngi-igenomes/test-data/proteinfold/db/alphafold_mini/mgnify/*" | ||
pdb70_path: "s3://ngi-igenomes/test-data/proteinfold/db/alphafold_mini/pdb70/**" | ||
pdb_mmcif_path: "s3://ngi-igenomes/test-data/proteinfold/db/alphafold_mini/pdb_mmcif/**" | ||
uniclust30_path: "s3://ngi-igenomes/test-data/proteinfold/db/alphafold_mini/uniclust30/**" | ||
uniref90_path: "s3://ngi-igenomes/test-data/proteinfold/db/alphafold_mini/uniref90/*" | ||
pdb_seqres_path: "s3://ngi-igenomes/test-data/proteinfold/db/alphafold_mini/pdb_seqres/*" | ||
uniprot_path: "s3://ngi-igenomes/test-data/proteinfold/db/alphafold_mini/uniprot/*" |
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process { | ||
withName: 'RUN_ALPHAFOLD2|RUN_ALPHAFOLD2_PRED|COLABFOLD_BATCH' { | ||
accelerator = 1 | ||
queue = <COMPUTE_QUEUE> | ||
} | ||
} |
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pipelines: | ||
- name: "nf-core-rnaseq" | ||
url: "https://github.com/nf-core/rnaseq" | ||
description: "RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control." | ||
workspace: "seqeralabs/showcase" | ||
compute-envs: "seqera_aws_ireland_fusionv2_nvme" | ||
revision: "3.12.0" | ||
profile: "test" | ||
labels: ["star_salmon", "yeast"] | ||
pre-run: "./pre-run.sh" | ||
params: | ||
outdir: "s3://seqeralabs-showcase/nf-core-rnaseq/results" | ||
overwrite: False | ||
- name: "nf-core-rnaseq-human" | ||
url: "https://github.com/nf-core/rnaseq" | ||
description: "RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control." | ||
workspace: "seqeralabs/showcase" | ||
compute-envs: "seqera_aws_ireland_fusionv2_nvme" | ||
revision: "3.12.0" | ||
labels: ["GRCh37", "star_salmon", "human"] | ||
pre-run: "./pre-run.sh" | ||
params: | ||
outdir: "s3://seqeralabs-showcase/nf-core-rnaseq-human/results" | ||
genome: "GRCh37" | ||
overwrite: False |
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pipelines: | ||
- name: "nf-core-sarek" | ||
url: "https://github.com/nf-core/sarek" | ||
description: "Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing." | ||
workspace: "seqeralabs/showcase" | ||
compute-envs: "seqera_azure_virginia_fusion" | ||
revision: "3.1.2" | ||
profile: "test" | ||
labels: ["germline", "variant-calling"] | ||
pre-run: "./pre-run.sh" | ||
params: | ||
outdir: "az://seqeralabs-showcase/nf-core-sarek/results" |
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pipelines: | ||
- name: "nf-core-viralrecon-illumina" | ||
url: "https://github.com/nf-core/viralrecon" | ||
description: "Assembly and intrahost/low-frequency variant calling for viral samples." | ||
workspace: "seqeralabs/showcase" | ||
compute-envs: "seqera_gcp_finland_fusion" | ||
revision: "2.6.0" | ||
profile: "test" | ||
labels: ["illumina", "sars-cov-2"] | ||
params: | ||
outdir: "gs://seqeralabs-showcase-eu-north-1/nf-core-viralrecon/illumina/results" | ||
assemblers: "spades,unicycler" | ||
overwrite: False | ||
- name: "nf-core-viralrecon-nanopore" | ||
url: "https://github.com/nf-core/viralrecon" | ||
description: "Assembly and intrahost/low-frequency variant calling for viral samples." | ||
workspace: "seqeralabs/showcase" | ||
compute-envs: "seqera_gcp_finland_fusion" | ||
revision: "2.6.0" | ||
profile: "test_nanopore" | ||
labels: ["nanopore", "sars-cov-2"] | ||
pre-run: "./pre-run.sh" | ||
params: | ||
outdir: "gs://seqeralabs-showcase-eu-north-1/nf-core-viralrecon/nanopore/results" | ||
overwrite: False |
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pipelines: | ||
- name: "nf-dragen" | ||
description: "Proof-of-concept Nextflow pipeline to run Illumina DRAGEN software." | ||
url: "https://github.com/seqera-labs/nf-dragen" | ||
workspace: "seqeralabs/showcase" | ||
compute-envs: "seqera_aws_ireland_dragen" | ||
revision: "master" | ||
profile: "test" | ||
labels: ["fpga", "variant-calling"] | ||
pre-run: "./pre-run.sh" | ||
params: | ||
outdir: "s3://nf-tower-bucket/nf-dragen/results" | ||
workspace-secrets: ["DRAGEN_PASSWORD", "DRAGEN_USERNAME"] | ||
overwrite: False |
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pipelines: | ||
- name: "nf-core-proteinfold" | ||
url: "https://github.com/nf-core/proteinfold" | ||
description: "Protein 3D structure prediction pipeline." | ||
workspace: "seqeralabs/showcase" | ||
compute-envs: "seqera_aws_ireland_fusionv2_nvme_gpu" | ||
revision: "1.0.0" | ||
profile: "test_full" | ||
labels: ["gpu", "structure-prediction"] | ||
pre-run: "./pre-run.sh" | ||
params-file: "./nf-core-proteinfold-params.yml" | ||
config: "./nf-core-proteinfold.config" | ||
overwrite: False | ||
- name: "nf-core-proteinfold_full_db" | ||
url: "https://github.com/nf-core/proteinfold" | ||
description: "Protein 3D structure prediction pipeline." | ||
workspace: "seqeralabs/showcase" | ||
compute-envs: "seqera_aws_ireland_fusionv2_nvme_gpu" | ||
revision: "1.0.0" | ||
labels: ["gpu", "structure-prediction"] | ||
pre-run: "./pre-run.sh" | ||
config: "./nf-core-proteinfold.config" | ||
params: | ||
outdir: "s3://seqeralabs-showcase/nf-core-proteinfold/db" | ||
use_gpu: true | ||
overwrite: False |
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pipelines: | ||
- name: "nf-sentieon" | ||
url: "https://github.com/seqeralabs/nf-sentieon" | ||
description: 'Proof-of-concept Nextflow pipeline to run Sentieon software.\nhttps://www.sentieon.com/' | ||
workspace: "seqeralabs/showcase" | ||
compute-envs: "seqera_aws_ireland_fusionv2_nvme" | ||
revision: "master" | ||
profile: "test" | ||
labels: ["variant-calling", "wgs"] | ||
pre-run: "./pre-run.sh" | ||
params: | ||
outdir: "s3://seqeralabs-showcase/nf-sentieon/results" | ||
overwrite: False |
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yum install jq -y | ||
export NXF_VER=$(curl -s https://api.github.com/repos/nextflow-io/nextflow/tags | jq -r '.[].name' | head -n 1 | cut -c2-) |
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