Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.2.0/modules/upload_microreact/main.nf @ 15:7c0407ebbdf3
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 17:55:16 -0400 |
| parents | a5f31c44f8c9 |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 process UPLOAD_MICROREACT { |
| kkonganti@11 | 2 tag "microreact_post.py" |
| kkonganti@11 | 3 label "process_pico" |
| kkonganti@11 | 4 |
| kkonganti@11 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) |
| kkonganti@11 | 6 conda (params.enable_conda ? "conda-forge::python=3.10 conda-forge::requests" : null) |
| kkonganti@11 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@11 | 8 'https://depot.galaxyproject.org/singularity/requests:2.26.0' : |
| kkonganti@11 | 9 'quay.io/biocontainers/requests:2.26.0' }" |
| kkonganti@11 | 10 |
| kkonganti@11 | 11 input: |
| kkonganti@11 | 12 path tree |
| kkonganti@11 | 13 path metadata |
| kkonganti@11 | 14 |
| kkonganti@11 | 15 output: |
| kkonganti@11 | 16 path "*.txt" , emit: url |
| kkonganti@11 | 17 path 'versions.yml', emit: versions |
| kkonganti@11 | 18 |
| kkonganti@11 | 19 when: |
| kkonganti@11 | 20 task.ext.when == null || task.ext.when |
| kkonganti@11 | 21 |
| kkonganti@11 | 22 script: |
| kkonganti@11 | 23 def args = task.ext.args ?: '' |
| kkonganti@11 | 24 """ |
| kkonganti@11 | 25 microreact_post.py \\ |
| kkonganti@11 | 26 $args \\ |
| kkonganti@11 | 27 -atp "${params.microreact_api_key}" \\ |
| kkonganti@11 | 28 -name "${params.microreact_tree_name}" \\ |
| kkonganti@11 | 29 -dir "." |
| kkonganti@11 | 30 |
| kkonganti@11 | 31 cat <<-END_VERSIONS > versions.yml |
| kkonganti@11 | 32 "${task.process}": |
| kkonganti@11 | 33 python: \$( python --version | sed 's/Python //g' ) |
| kkonganti@11 | 34 END_VERSIONS |
| kkonganti@11 | 35 """ |
| kkonganti@11 | 36 |
| kkonganti@11 | 37 } |