Update pipeline JSON files

adamrtalbot · May 23, 2023 · 9d65c23 · 9d65c23
1 parent a4e2f07
commit 9d65c23
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Showing 8 changed files with 26 additions and 24 deletions.
diff --git a/pipelines/hello.json b/pipelines/hello.json
@@ -5,6 +5,8 @@
     "revision": "master",
     "userSecrets": [],
     "workspaceSecrets": [],
+    "configText": "",
+    "preRunScript": "export NXF_VER=23.05.0-edge",
     "resume": false,
     "pullLatest": false,
     "stubRun": false

diff --git a/pipelines/nf-core-proteinfold.json b/pipelines/nf-core-proteinfold.json
@@ -8,8 +8,9 @@
     ],
     "userSecrets": [],
     "workspaceSecrets": [],
-    "configText": "process {\n    errorStrategy = 'retry'\n    maxRetries = 1\n\n    withName: 'RUN_ALPHAFOLD2|RUN_ALPHAFOLD2_PRED|RUN_ALPHAFOLD2_MSA|COLABFOLD_BATCH' {\n        accelerator = 1\n        queue = 'TowerForge-6IOueWtY2YO2fmo4ES5M64-work'\n    }\n}",
-    "paramsText": "outdir: 's3://seqeralabs-showcase/nf-core-proteinfold/results_2023_02_20'\nuse_gpu: true",
+    "configText": "process {\n    withName: 'RUN_ALPHAFOLD2|RUN_ALPHAFOLD2_PRED|COLABFOLD_BATCH' {\n        accelerator = 1\n        queue = 'TowerForge-1JPnaIxHRoMbhq6TNLgUF6-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/results'\nuse_gpu: true",
+    "preRunScript": "export NXF_VER=23.05.0-edge",
     "resume": false,
     "pullLatest": false,
     "stubRun": false

diff --git a/pipelines/nf-core-rnaseq.json b/pipelines/nf-core-rnaseq.json
@@ -2,14 +2,15 @@
   "description": "RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.",
   "launch": {
     "pipeline": "https://github.com/nf-core/rnaseq",
-    "revision": "3.10.1",
+    "revision": "3.11.2",
     "configProfiles": [
       "test"
     ],
     "userSecrets": [],
     "workspaceSecrets": [],
-    "configText": "process.errorStrategy = 'retry'\nprocess.maxRetries = 3",
-    "paramsText": "outdir: 's3://seqeralabs-showcase/nf-core-rnaseq/results_2023_02_20'",
+    "configText": "",
+    "paramsText": "input: 'https://api.tower.nf/workspaces/138659136604200/datasets/7DPM3wJTa6zDROKw6SGFLg/v/2/n/rnaseq-samples.csv'\noutdir: 's3://seqeralabs-showcase/nf-core-rnaseq/results'",
+    "preRunScript": "export NXF_VER=23.05.0-edge",
     "resume": false,
     "pullLatest": false,
     "stubRun": false

diff --git a/pipelines/nf-core-sarek.json b/pipelines/nf-core-sarek.json
@@ -6,10 +6,9 @@
     "configProfiles": [
       "test"
     ],
-    "userSecrets": [],
-    "workspaceSecrets": [],
-    "configText": "process.errorStrategy = 'retry'\nprocess.maxRetries = 3",
-    "paramsText": "outdir: 's3://seqeralabs-showcase/nf-core-sarek/results_2023_02_20'",
+    "configText": "",
+    "paramsText": "input: 'https://api.tower.nf/workspaces/138659136604200/datasets/31MNGqAiTAz464AECz5Ujr/v/1/n/sarek-samples.csv'\noutdir: 'az://seqeralabs-showcase/nf-core-sarek/results'",
+    "preRunScript": "export NXF_VER=23.05.0-edge",
     "resume": false,
     "pullLatest": false,
     "stubRun": false

diff --git a/pipelines/nf-core-viralrecon-illumina.json b/pipelines/nf-core-viralrecon-illumina.json
@@ -2,14 +2,13 @@
   "description": "Pipeline for assembly and intrahost/low-frequency variant calling for viral samples.",
   "launch": {
     "pipeline": "https://github.com/nf-core/viralrecon",
-    "revision": "2.5",
+    "revision": "2.6.0",
     "configProfiles": [
       "test"
     ],
-    "userSecrets": [],
-    "workspaceSecrets": [],
-    "configText": "process.errorStrategy = 'retry'\nprocess.maxRetries = 3",
-    "paramsText": "outdir: 's3://seqeralabs-showcase/nf-core-viralrecon/illumina/results_2023_02_20'",
+    "configText": "",
+    "paramsText": "input: 'https://api.tower.nf/workspaces/138659136604200/datasets/4GC5jTkiloEIYBscThIf7r/v/1/n/viralrecon-illumina-samples.csv'\noutdir: 'gs://seqeralabs-showcase/nf-core-viralrecon/illumina/results'",
+    "preRunScript": "export NXF_VER=23.05.0-edge",
     "resume": false,
     "pullLatest": false,
     "stubRun": false

diff --git a/pipelines/nf-core-viralrecon-nanopore.json b/pipelines/nf-core-viralrecon-nanopore.json
@@ -2,14 +2,13 @@
   "description": "Pipeline for assembly and intrahost/low-frequency variant calling for viral samples.",
   "launch": {
     "pipeline": "https://github.com/nf-core/viralrecon",
-    "revision": "2.5",
+    "revision": "2.6.0",
     "configProfiles": [
       "test_nanopore"
     ],
-    "userSecrets": [],
-    "workspaceSecrets": [],
-    "configText": "process.errorStrategy = 'retry'\nprocess.maxRetries = 3",
-    "paramsText": "outdir: 's3://seqeralabs-showcase/nf-core-viralrecon/nanopore/results_2023_02_20'",
+    "configText": "",
+    "paramsText": "input: 'https://api.tower.nf/workspaces/138659136604200/datasets/443ChPTGqwQZwl7xrvvGpP/v/1/n/viralrecon-nanopore-samples.csv'\noutdir: 'gs://seqeralabs-showcase/nf-core-viralrecon/nanopore/results'",
+    "preRunScript": "export NXF_VER=23.05.0-edge",
     "resume": false,
     "pullLatest": false,
     "stubRun": false

diff --git a/pipelines/nf-dragen.json b/pipelines/nf-dragen.json
@@ -11,10 +11,10 @@
       "DRAGEN_PASSWORD",
       "DRAGEN_USERNAME"
     ],
-    "configText": "process.errorStrategy = 'retry'\nprocess.maxRetries = 3",
-    "paramsText": "outdir: 's3://nf-tower-bucket/nf-dragen/results_2023_02_20'",
+    "configText": "",
+    "paramsText": "input: 'https://api.tower.nf/workspaces/138659136604200/datasets/TqOcEbEQEvd4inHuRPUsV/v/1/n/dragen-samples.csv'\noutdir: 's3://nf-tower-bucket/nf-dragen/results'",
     "resume": false,
-    "pullLatest": true,
+    "pullLatest": false,
     "stubRun": false
   }
 }
diff --git a/pipelines/nf-sentieon.json b/pipelines/nf-sentieon.json
@@ -10,8 +10,9 @@
     "workspaceSecrets": [
       "SENTIEON_LICENSE_BASE64"
     ],
-    "configText": "process.errorStrategy = 'retry'\nprocess.maxRetries = 3",
-    "paramsText": "outdir: 's3://seqeralabs-showcase/nf-sentieon/results_2023_02_20'",
+    "configText": "",
+    "paramsText": "input: 'https://api.tower.nf/workspaces/138659136604200/datasets/2K6cdA0sRDw7Bauc67CmIT/v/1/n/sentieon-samples.csv'\noutdir: 's3://seqeralabs-showcase/nf-sentieon/results'",
+    "preRunScript": "export NXF_VER=23.05.0-edge",
     "resume": false,
     "pullLatest": false,
     "stubRun": false