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S3 #4

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d4ba4f1
Update .gitignore
tatianawoller Dec 5, 2024
a51a32c
change HPC VSC with Bugra
tatianawoller Dec 5, 2024
98de69d
Delete bfflow directory
tatianawoller Dec 5, 2024
1286230
modification bfflow for HPC VSC with bugra
tatianawoller Dec 5, 2024
a55ba9e
nextflow.config not using institutional config
tatianawoller Dec 5, 2024
36a5f67
s3 test
tatianawoller Dec 5, 2024
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -7,3 +7,4 @@ testing/
testing*
*.pyc
null/
.singularityCache/
2 changes: 1 addition & 1 deletion main.nf
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Expand Up @@ -12,7 +12,7 @@
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
nextflow.enable.moduleBinaries = true
//nextflow.enable.moduleBinaries = true

include { BATCHCONVERT_TO_OMETIFF } from './workflows/bftools.nf'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_demo_workflow_pipeline'
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2 changes: 1 addition & 1 deletion modules/nf-core/bfconvert/main.nf
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35 changes: 33 additions & 2 deletions nextflow.config
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Expand Up @@ -28,7 +28,8 @@ params {
bigtiff = null
pyramid_resolutions = null
pyramid_scale = null
// singularityCache = "${baseDir}/.singularityCache"
singularityCache = "/dodrio/scratch/projects/2024_300/twoller/.singularityCache"
// cluster_options = "--mem-per-cpu=3140 --cpus-per-task=4 "

// Boilerplate options
outdir = null
Expand All @@ -49,6 +50,14 @@ params {
includeConfig 'conf/base.config'
includeConfig 'conf/modules.config'

aws {
accessKey='hack-nxf'
secretKey='PX25b35=w<'
client {
endpoint="https://s3.embl.de"
s3PathStyleAccess=true
}
}
profiles {
debug {
dumpHashes = true
Expand Down Expand Up @@ -98,8 +107,30 @@ profiles {
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
//singularity.cacheDir = "${params.singularityCache}"
singularity.cacheDir = "${params.singularityCache}"
singularity.autoMounts = true
process {
executor = 'local'
containerOptions = "-B ${baseDir} -B $PWD -B $HOME"
}
}
cluster {

singularity.enabled = true
singularity.autoMounts = true
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
singularity.cacheDir = "${params.singularityCache}"
singularity.autoMounts = true
process {
executor = 'slurm'
// clusterOptions = "${params.cluster_options}"
containerOptions = "-B ${baseDir} -B $PWD -B $HOME"
}
}
podman {
podman.enabled = true
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Binary file added s3/nextflow-hackathon/test/data_bfflow/res_from_tiffs/bfconvert_output/example.ome.tiff
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3 changes: 3 additions & 0 deletions ...ckathon/test/data_bfflow/res_from_tiffs/pipeline_info/demo_workflow_software_versions.yml
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@@ -0,0 +1,3 @@
Workflow:
kbestak/demo_workflow: v1.0.0dev
Nextflow: 24.04.4
1,062 changes: 1,062 additions & 0 deletions ...n/test/data_bfflow/res_from_tiffs/pipeline_info/execution_report_2024-12-05_16-38-35.html
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1,040 changes: 1,040 additions & 0 deletions ...n/test/data_bfflow/res_from_tiffs/pipeline_info/execution_report_2024-12-05_16-40-18.html
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223 changes: 223 additions & 0 deletions ...test/data_bfflow/res_from_tiffs/pipeline_info/execution_timeline_2024-12-05_16-38-35.html
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223 changes: 223 additions & 0 deletions ...test/data_bfflow/res_from_tiffs/pipeline_info/execution_timeline_2024-12-05_16-40-18.html
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1 change: 1 addition & 0 deletions ...hon/test/data_bfflow/res_from_tiffs/pipeline_info/execution_trace_2024-12-05_16-38-35.txt
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@@ -0,0 +1 @@
task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
2 changes: 2 additions & 0 deletions ...hon/test/data_bfflow/res_from_tiffs/pipeline_info/execution_trace_2024-12-05_16-40-18.txt
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task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
1 c7/2cedfd 9681378 BATCHCONVERT_TO_OMETIFF:BFCONVERT (example) COMPLETED 0 2024-12-05 16:40:31.700 8.6s 4s 72.9% 171.9 MB 3 GB 38.4 MB 1.9 MB
32 changes: 32 additions & 0 deletions ...w-hackathon/test/data_bfflow/res_from_tiffs/pipeline_info/params_2024-12-05_16-38-43.json
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{
"input": "../data_bfflow/test.csv",
"noflat": null,
"series": null,
"timepoint": null,
"channel": null,
"z": null,
"range": null,
"tiley": null,
"tilex": null,
"crop": null,
"compression": null,
"overwrite": null,
"nooverwrite": null,
"nolookup": null,
"bigtiff": null,
"pyramid_resolutions": null,
"pyramid_scale": null,
"singularityCache": "/dodrio/scratch/projects/2024_300/twoller/.singularityCache",
"singularity-cache": "/dodrio/scratch/projects/2024_300/twoller/.singularityCache",
"cluster_options": "--mem-per-cpu=3140 --cpus-per-task=4 ",
"outdir": "s3//nextflow-hackathon/test/data_bfflow/res_from_tiffs",
"publish_dir_mode": "copy",
"monochrome_logs": false,
"help": false,
"help_full": false,
"show_hidden": false,
"version": false,
"pipelines_testdata_base_path": "https://raw.githubusercontent.com/nf-core/test-datasets/",
"trace_report_suffix": "2024-12-05_16-38-35",
"validate_params": true
}
31 changes: 31 additions & 0 deletions ...w-hackathon/test/data_bfflow/res_from_tiffs/pipeline_info/params_2024-12-05_16-40-28.json
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@@ -0,0 +1,31 @@
{
"input": "../data_bfflow/test.csv",
"noflat": null,
"series": null,
"timepoint": null,
"channel": null,
"z": null,
"range": null,
"tiley": null,
"tilex": null,
"crop": null,
"compression": null,
"overwrite": null,
"nooverwrite": null,
"nolookup": null,
"bigtiff": null,
"pyramid_resolutions": null,
"pyramid_scale": null,
"singularityCache": "/dodrio/scratch/projects/2024_300/twoller/.singularityCache",
"singularity-cache": "/dodrio/scratch/projects/2024_300/twoller/.singularityCache",
"outdir": "s3//nextflow-hackathon/test/data_bfflow/res_from_tiffs",
"publish_dir_mode": "copy",
"monochrome_logs": false,
"help": false,
"help_full": false,
"show_hidden": false,
"version": false,
"pipelines_testdata_base_path": "https://raw.githubusercontent.com/nf-core/test-datasets/",
"trace_report_suffix": "2024-12-05_16-40-18",
"validate_params": true
}
43 changes: 43 additions & 0 deletions ...athon/test/data_bfflow/res_from_tiffs/pipeline_info/pipeline_dag_2024-12-05_16-38-35.html
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<!--
~ Copyright 2013-2024, Seqera Labs
~
~ Licensed under the Apache License, Version 2.0 (the "License");
~ you may not use this file except in compliance with the License.
~ You may obtain a copy of the License at
~
~ http://www.apache.org/licenses/LICENSE-2.0
~
~ Unless required by applicable law or agreed to in writing, software
~ distributed under the License is distributed on an "AS IS" BASIS,
~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
~ See the License for the specific language governing permissions and
~ limitations under the License.
-->
<html>
<head>
<meta name="viewport" content="width=device-width, user-scalable=no, initial-scale=1, maximum-scale=1">
</head>
<body>
<pre class="mermaid" style="text-align: center;">
flowchart TB
subgraph " "
v2["Channel.fromList"]
end
subgraph BATCHCONVERT_TO_OMETIFF
v5([BFCONVERT])
v3(( ))
end
subgraph " "
v6[" "]
end
v2 --> v3
v3 --> v5
v5 --> v6

</pre>
<script type="module">
import mermaid from 'https://cdn.jsdelivr.net/npm/mermaid@10/dist/mermaid.esm.min.mjs';
mermaid.initialize({ startOnLoad: true });
</script>
</body>
</html>
43 changes: 43 additions & 0 deletions ...athon/test/data_bfflow/res_from_tiffs/pipeline_info/pipeline_dag_2024-12-05_16-40-18.html
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@@ -0,0 +1,43 @@
<!--
~ Copyright 2013-2024, Seqera Labs
~
~ Licensed under the Apache License, Version 2.0 (the "License");
~ you may not use this file except in compliance with the License.
~ You may obtain a copy of the License at
~
~ http://www.apache.org/licenses/LICENSE-2.0
~
~ Unless required by applicable law or agreed to in writing, software
~ distributed under the License is distributed on an "AS IS" BASIS,
~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
~ See the License for the specific language governing permissions and
~ limitations under the License.
-->
<html>
<head>
<meta name="viewport" content="width=device-width, user-scalable=no, initial-scale=1, maximum-scale=1">
</head>
<body>
<pre class="mermaid" style="text-align: center;">
flowchart TB
subgraph " "
v2["Channel.fromList"]
end
subgraph BATCHCONVERT_TO_OMETIFF
v5([BFCONVERT])
v3(( ))
end
subgraph " "
v6[" "]
end
v2 --> v3
v3 --> v5
v5 --> v6

</pre>
<script type="module">
import mermaid from 'https://cdn.jsdelivr.net/npm/mermaid@10/dist/mermaid.esm.min.mjs';
mermaid.initialize({ startOnLoad: true });
</script>
</body>
</html>
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