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comparison 0.2.0/modules/upload_microreact/main.nf @ 11:a5f31c44f8c9

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planemo upload
author kkonganti
date Mon, 15 Jul 2024 16:11:44 -0400
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10:ddf7a172bf30 11:a5f31c44f8c9
1 process UPLOAD_MICROREACT {
2 tag "microreact_post.py"
3 label "process_pico"
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
6 conda (params.enable_conda ? "conda-forge::python=3.10 conda-forge::requests" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/requests:2.26.0' :
9 'quay.io/biocontainers/requests:2.26.0' }"
10
11 input:
12 path tree
13 path metadata
14
15 output:
16 path "*.txt" , emit: url
17 path 'versions.yml', emit: versions
18
19 when:
20 task.ext.when == null || task.ext.when
21
22 script:
23 def args = task.ext.args ?: ''
24 """
25 microreact_post.py \\
26 $args \\
27 -atp "${params.microreact_api_key}" \\
28 -name "${params.microreact_tree_name}" \\
29 -dir "."
30
31 cat <<-END_VERSIONS > versions.yml
32 "${task.process}":
33 python: \$( python --version | sed 's/Python //g' )
34 END_VERSIONS
35 """
36
37 }