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feat: add newer datasets, update pipelines, add yaml
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sample,fastq_1,fastq_2,strandedness,run_accession,experiment_accession,sample_accession,secondary_sample_accession,study_accession,secondary_study_accession,submission_accession,run_alias,experiment_alias,sample_alias,study_alias,library_layout,library_selection,library_source,library_strategy,library_name,instrument_model,instrument_platform,base_count,read_count,tax_id,scientific_name,sample_title,experiment_title,study_title,sample_description,fastq_md5,fastq_bytes,fastq_ftp,fastq_galaxy,fastq_aspera | ||
SRX21750941,s3://seqeralabs-showcase/nf-core-fetchngs/SRP459762/results/fastq/SRX21750941_SRR26033656_1.fastq.gz,s3://seqeralabs-showcase/nf-core-fetchngs/SRP459762/results/fastq/SRX21750941_SRR26033656_2.fastq.gz,auto,SRR26033656,SRX21750941,SAMN37353910,SRS18858468,PRJNA1014965,SRP459762,SRA1710039,MEC_T_07_1.fastq.gz,MEC_T_07,,PRJNA1014965,PAIRED,unspecified,TRANSCRIPTOMIC,RNA-Seq,MEC_T_07,Illumina HiSeq 2500,ILLUMINA,9105149798,45074999,9606,Homo sapiens,,Illumina HiSeq 2500 sequencing: RNA-Seq of mucoepidermoid carcinoma,Immunological subtyping of salivary gland cancer identifies histological origin-specific tumor immune microenvironment,,a4e3385ac9b33a12a2648687af5a9eda;1cba4d7de8569bc84216d0d6f5ba19a1,1734457262;1749369782,ftp.sra.ebi.ac.uk/vol1/fastq/SRR260/056/SRR26033656/SRR26033656_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR260/056/SRR26033656/SRR26033656_2.fastq.gz,ftp.sra.ebi.ac.uk/vol1/fastq/SRR260/056/SRR26033656/SRR26033656_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR260/056/SRR26033656/SRR26033656_2.fastq.gz,fasp.sra.ebi.ac.uk:/vol1/fastq/SRR260/056/SRR26033656/SRR26033656_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR260/056/SRR26033656/SRR26033656_2.fastq.gz | ||
SRX21750942,s3://seqeralabs-showcase/nf-core-fetchngs/SRP459762/results/fastq/SRX21750942_SRR26033655_1.fastq.gz,s3://seqeralabs-showcase/nf-core-fetchngs/SRP459762/results/fastq/SRX21750942_SRR26033655_2.fastq.gz,auto,SRR26033655,SRX21750942,SAMN37353911,SRS18858470,PRJNA1014965,SRP459762,SRA1710039,MEC_T_08_1.fastq.gz,MEC_T_08,,PRJNA1014965,PAIRED,unspecified,TRANSCRIPTOMIC,RNA-Seq,MEC_T_08,Illumina HiSeq 2500,ILLUMINA,7291499060,36096530,9606,Homo sapiens,,Illumina HiSeq 2500 sequencing: RNA-Seq of mucoepidermoid carcinoma,Immunological subtyping of salivary gland cancer identifies histological origin-specific tumor immune microenvironment,,37c4046ba9128693ff685fd1a8f867da;2aa0babe90e17ed58636909b11d0a4eb,1331451936;1345825378,ftp.sra.ebi.ac.uk/vol1/fastq/SRR260/055/SRR26033655/SRR26033655_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR260/055/SRR26033655/SRR26033655_2.fastq.gz,ftp.sra.ebi.ac.uk/vol1/fastq/SRR260/055/SRR26033655/SRR26033655_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR260/055/SRR26033655/SRR26033655_2.fastq.gz,fasp.sra.ebi.ac.uk:/vol1/fastq/SRR260/055/SRR26033655/SRR26033655_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR260/055/SRR26033655/SRR26033655_2.fastq.gz | ||
SRX21750943,s3://seqeralabs-showcase/nf-core-fetchngs/SRP459762/results/fastq/SRX21750943_SRR26033654_1.fastq.gz,s3://seqeralabs-showcase/nf-core-fetchngs/SRP459762/results/fastq/SRX21750943_SRR26033654_2.fastq.gz,auto,SRR26033654,SRX21750943,SAMN37353912,SRS18858471,PRJNA1014965,SRP459762,SRA1710039,MEC_T_09_1.fastq.gz,MEC_T_09,,PRJNA1014965,PAIRED,unspecified,TRANSCRIPTOMIC,RNA-Seq,MEC_T_09,Illumina HiSeq 2500,ILLUMINA,7761595884,38423742,9606,Homo sapiens,,Illumina HiSeq 2500 sequencing: RNA-Seq of mucoepidermoid carcinoma,Immunological subtyping of salivary gland cancer identifies histological origin-specific tumor immune microenvironment,,d7a91ce3b764c79722d4f36ec5713efa;e42d3c993a18108a5258af65141c580f,1170104300;1203799314,ftp.sra.ebi.ac.uk/vol1/fastq/SRR260/054/SRR26033654/SRR26033654_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR260/054/SRR26033654/SRR26033654_2.fastq.gz,ftp.sra.ebi.ac.uk/vol1/fastq/SRR260/054/SRR26033654/SRR26033654_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR260/054/SRR26033654/SRR26033654_2.fastq.gz,fasp.sra.ebi.ac.uk:/vol1/fastq/SRR260/054/SRR26033654/SRR26033654_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR260/054/SRR26033654/SRR26033654_2.fastq.gz | ||
SRX21750944,s3://seqeralabs-showcase/nf-core-fetchngs/SRP459762/results/fastq/SRX21750944_SRR26033653_1.fastq.gz,s3://seqeralabs-showcase/nf-core-fetchngs/SRP459762/results/fastq/SRX21750944_SRR26033653_2.fastq.gz,auto,SRR26033653,SRX21750944,SAMN37353913,SRS18858472,PRJNA1014965,SRP459762,SRA1710039,MEC_T_10_1.fastq.gz,MEC_T_10,,PRJNA1014965,PAIRED,unspecified,TRANSCRIPTOMIC,RNA-Seq,MEC_T_10,Illumina HiSeq 2500,ILLUMINA,9238355264,45734432,9606,Homo sapiens,,Illumina HiSeq 2500 sequencing: RNA-Seq of mucoepidermoid carcinoma,Immunological subtyping of salivary gland cancer identifies histological origin-specific tumor immune microenvironment,,1a63023afeca02cd10271a20385424b1;0939823df564a6d14b61eb45581994e8,1768219705;1783586223,ftp.sra.ebi.ac.uk/vol1/fastq/SRR260/053/SRR26033653/SRR26033653_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR260/053/SRR26033653/SRR26033653_2.fastq.gz,ftp.sra.ebi.ac.uk/vol1/fastq/SRR260/053/SRR26033653/SRR26033653_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR260/053/SRR26033653/SRR26033653_2.fastq.gz,fasp.sra.ebi.ac.uk:/vol1/fastq/SRR260/053/SRR26033653/SRR26033653_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR260/053/SRR26033653/SRR26033653_2.fastq.gz | ||
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SRR26033653 | ||
SRR26033654 | ||
SRR26033655 | ||
SRR26033656 |
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{ | ||
"description": "Pipeline to fetch metadata and raw FastQ files from public and private databases\n\n", | ||
"launch": { | ||
"pipeline": "https://github.com/nf-core/fetchngs", | ||
"revision": "1.10.1", | ||
"configProfiles": [ | ||
"test" | ||
], | ||
"userSecrets": [], | ||
"workspaceSecrets": [], | ||
"configText": "", | ||
"paramsText": "outdir: 's3://seqeralabs-showcase/nf-core-fetchngs/results'\nforce_sratools_download: true\nnf_core_pipeline: 'rnaseq'", | ||
"preRunScript": "yum install jq -y\nexport NXF_VER=$(curl -s https://api.github.com/repos/nextflow-io/nextflow/tags | jq -r '.[].name' | head -n 1 | cut -c2-)", | ||
"resume": false, | ||
"pullLatest": false, | ||
"stubRun": false | ||
} | ||
} |
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{ | ||
"description": "", | ||
"launch": { | ||
"pipeline": "https://github.com/nf-core/proteinfold", | ||
"revision": "1.0.0", | ||
"configProfiles": [], | ||
"userSecrets": [], | ||
"workspaceSecrets": [], | ||
"configText": "process {\n withName: 'RUN_ALPHAFOLD2|RUN_ALPHAFOLD2_PRED|COLABFOLD_BATCH' {\n accelerator = 1\n queue = 'TowerForge-5ZfzTbavbsB9Tx7YRr2ut0-work'\n }\n}", | ||
"paramsText": "input: 'https://api.tower.nf/workspaces/138659136604200/datasets/5Ig3IWRgjlgVjpURNF6CSN/v/1/n/samplesheet.csv'\noutdir: 's3://seqeralabs-showcase/nf-core-proteinfold/db'\nuse_gpu: true", | ||
"preRunScript": "yum install jq -y\nexport NXF_VER=$(curl -s https://api.github.com/repos/nextflow-io/nextflow/tags | jq -r '.[].name' | head -n 1 | cut -c2-)", | ||
"resume": false, | ||
"pullLatest": false, | ||
"stubRun": false | ||
} | ||
} |
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{ | ||
"launch": { | ||
"pipeline": "https://github.com/nf-core/rnaseq", | ||
"revision": "3.12.0", | ||
"configProfiles": [], | ||
"userSecrets": [], | ||
"workspaceSecrets": [], | ||
"configText": "", | ||
"paramsText": "genome: 'GRCh37'\noutdir: 's3://seqeralabs-showcase/nf-core-rnaseq/results'\n\n", | ||
"preRunScript": "yum install jq -y\nexport NXF_VER=$(curl -s https://api.github.com/repos/nextflow-io/nextflow/tags | jq -r '.[].name' | head -n 1 | cut -c2-)", | ||
"resume": false, | ||
"pullLatest": false, | ||
"stubRun": false | ||
} | ||
} |
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@@ -1,16 +1,18 @@ | ||
{ | ||
"description": "Pipeline for assembly and intrahost/low-frequency variant calling for viral samples.", | ||
"launch": { | ||
"pipeline": "https://github.com/nf-core/viralrecon", | ||
"revision": "2.6.0", | ||
"configProfiles": [ | ||
"test" | ||
], | ||
"configText": "", | ||
"paramsText": "input: 'https://api.tower.nf/workspaces/138659136604200/datasets/4GC5jTkiloEIYBscThIf7r/v/1/n/viralrecon-illumina-samples.csv'\noutdir: 'gs://seqeralabs-showcase-eu-north-1/nf-core-viralrecon/illumina/results'", | ||
"towerConfig": "", | ||
"paramsText": "input: 'https://api.tower.nf/workspaces/138659136604200/datasets/4GC5jTkiloEIYBscThIf7r/v/1/n/viralrecon-illumina-samples.csv'\noutdir: 'gs://seqeralabs-showcase-eu-north-1/nf-core-viralrecon/illumina/results'\nassemblers: 'spades,unicycler'", | ||
"preRunScript": "yum install jq -y\nexport NXF_VER=$(curl -s https://api.github.com/repos/nextflow-io/nextflow/tags | jq -r '.[].name' | head -n 1 | cut -c2-)", | ||
"resume": false, | ||
"pullLatest": false, | ||
"stubRun": false | ||
"stubRun": false, | ||
"optimizationId": "jnQkdRdVKPsdUuNC", | ||
"optimizationTargets": "pcpu, peak_rss, realtime" | ||
} | ||
} |
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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: True | ||
- name: 'seqera_aws_ireland_fusionv2_nvme' | ||
workspace: 'seqeralabs/showcase' | ||
credentials: 'seqera_aws_development_credentials' | ||
wait: 'AVAILABLE' | ||
file-path: './compute-envs/seqera_aws_ireland_fusionv2_nvme.json' | ||
overwrite: True | ||
- name: 'seqera_aws_ireland_fusionv2_nvme_gpu' | ||
workspace: 'seqeralabs/showcase' | ||
credentials: 'seqera_aws_development_credentials' | ||
wait: 'AVAILABLE' | ||
file-path: './compute-envs/seqera_aws_ireland_fusionv2_nvme_gpu.json' | ||
overwrite: True | ||
- name: 'seqera_aws_ireland_s3' | ||
workspace: 'seqeralabs/showcase' | ||
wait: 'AVAILABLE' | ||
file-path: './compute-envs/seqera_aws_ireland_s3.json' | ||
overwrite: True | ||
- name: 'seqera_azure_virginia' | ||
workspace: 'seqeralabs/showcase' | ||
wait: 'AVAILABLE' | ||
file-path: './compute-envs/seqera_azure_virginia.json' | ||
overwrite: True | ||
- name: 'seqera_gcp_finland' | ||
workspace: 'seqeralabs/showcase' | ||
wait: 'AVAILABLE' | ||
file-path: './compute-envs/seqera_gcp_finland.json' | ||
overwrite: True | ||
- name: 'seqera_slurm' | ||
workspace: 'seqeralabs/showcase' | ||
wait: 'AVAILABLE' | ||
file-path: './compute-envs/seqera_slurm.json' | ||
overwrite: True | ||
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: True | ||
- 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: True | ||
- 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: True | ||
- 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: True | ||
- 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: True | ||
- 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: True | ||
- 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: True | ||
- 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: True | ||
- 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: True | ||
pipelines: | ||
- name: 'hello' | ||
workspace: 'seqerakit-e2e/showcase' | ||
compute-envs: 'seqera_aws_ireland_fusionv2_nvme' | ||
file-path: './pipelines/hello.json' | ||
overwrite: True | ||
- name: 'nf-core-proteinfold' | ||
workspace: 'seqerakit-e2e/showcase' | ||
compute-envs: 'seqera_aws_ireland_fusionv2_nvme_gpu' | ||
file-path: './pipelines/nf-core-proteinfold.json' | ||
overwrite: True | ||
- name: 'nf-core-rnaseq' | ||
workspace: 'seqerakit-e2e/showcase' | ||
compute-envs: 'seqera_aws_ireland_fusionv2_nvme' | ||
file-path: './pipelines/nf-core-rnaseq.json' | ||
overwrite: True | ||
- name: 'nf-core-sarek' | ||
workspace: 'seqerakit-e2e/showcase' | ||
compute-envs: 'seqera_aws_ireland_fusionv2_nvme' | ||
file-path: './pipelines/nf-core-sarek.json' | ||
overwrite: True | ||
- name: 'nf-dragen' | ||
workspace: 'seqerakit-e2e/showcase' | ||
compute-envs: 'seqera_aws_ireland_dragen' | ||
file-path: './pipelines/nf-dragen.json' | ||
overwrite: True | ||
- name: 'nf-sentieon' | ||
workspace: 'seqerakit-e2e/showcase' | ||
compute-envs: 'seqera_aws_ireland_fusionv2_nvme' | ||
file-path: './pipelines/nf-sentieon.json' | ||
overwrite: True | ||
- name: 'nf-core-viralrecon-illumina' | ||
workspace: 'seqerakit-e2e/showcase' | ||
compute-envs: 'seqera_gcp_finland' | ||
file-path: './pipelines/nf-core-viralrecon-illumina.json' | ||
overwrite: True | ||
- name: 'nf-core-viralrecon-nanopore' | ||
workspace: 'seqerakit-e2e/showcase' | ||
compute-envs: 'seqera_gcp_finland' | ||
file-path: './pipelines/nf-core-viralrecon-nanopore.json' | ||
overwrite: True | ||
- name: 'nf-core-fetchngs' | ||
workspace: 'seqerakit-e2e/showcase' | ||
compute-envs: 'seqera_aws_ireland_fusionv2_nvme' | ||
file-path: './pipelines/nf-core-fetchngs.json' | ||
overwrite: True | ||
- name: 'nf-core-rnaseq-human' | ||
workspace: 'seqerakit-e2e/showcase' | ||
compute-envs: 'seqera_aws_ireland_fusionv2_nvme' | ||
file-path: './pipelines/nf-core-rnaseq-human.json' | ||
overwrite: True |