From 4dfa035dc2cca0f86460ac06df1d96dd56382560 Mon Sep 17 00:00:00 2001 From: Nathan Thorpe Date: Fri, 28 Nov 2025 16:29:33 -0800 Subject: [PATCH 1/2] update fetchngs and parameters --- nf-core/fetchngs/1.7/process-definition.json | 2 +- nf-core/fetchngs/1.7/process-input.json | 5 +++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/nf-core/fetchngs/1.7/process-definition.json b/nf-core/fetchngs/1.7/process-definition.json index 3d926ab..e9fb9d2 100644 --- a/nf-core/fetchngs/1.7/process-definition.json +++ b/nf-core/fetchngs/1.7/process-definition.json @@ -39,7 +39,7 @@ "repository": "GITHUBPUBLIC", "script": "main.nf", "uri": "nf-core/fetchngs", - "version": "1.10.0" + "version": "1.12.0" }, "usesSampleSheet": false, "computeDefaults": [ diff --git a/nf-core/fetchngs/1.7/process-input.json b/nf-core/fetchngs/1.7/process-input.json index 31ce194..f8c1775 100644 --- a/nf-core/fetchngs/1.7/process-input.json +++ b/nf-core/fetchngs/1.7/process-input.json @@ -1,8 +1,9 @@ { - "input": "$.params.dataset.s3|/|$.params.dataset.paramJson.input", + "input": "$.dataset.params.input", + "download_method": "$.dataset.params.download_method", + "dbgap_key": "$.dataset.params.dbgap_key", "nf_core_pipeline": "$.dataset.params.pipeline", "outdir": "$.dataset.dataPath", - "input_type": "sra", "hostnames": "test", "schema_ignore_params": "hostnames" } From 31081dc9c19fa67baa618a8ffa6a2123ef14fb20 Mon Sep 17 00:00:00 2001 From: Nathan Thorpe Date: Sun, 30 Nov 2025 17:04:19 -0800 Subject: [PATCH 2/2] remove old param --- nf-core/fetchngs/1.7/process-compute.config | 2 -- 1 file changed, 2 deletions(-) diff --git a/nf-core/fetchngs/1.7/process-compute.config b/nf-core/fetchngs/1.7/process-compute.config index 7c402ca..311a7a8 100644 --- a/nf-core/fetchngs/1.7/process-compute.config +++ b/nf-core/fetchngs/1.7/process-compute.config @@ -1,5 +1,3 @@ -params.force_sratools_download = true - process { errorStrategy = { task.attempt <= 5 ? 'retry' : 'terminate' } maxRetries = 2