Eklipse topics migration #11125
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
| channels: | ||
| - bioconda | ||
| - conda-forge | ||
| dependencies: | ||
| - bioconda::eklipse=1.8=hdfd78af_2 |
|
Contributor
There was a problem hiding this comment. You can run nextflow lint -format -sort-declarations -spaces 4 -harshil-alignmenton this file to clean this up nicely.
Contributor
There was a problem hiding this comment. If you removed conda support then you need to add a warning that conda is not supported by this module. But I would rather try and investigate what happens with conda and why it does not work
Contributor
There was a problem hiding this comment. I looked into it and the bioconda recipe is broken. This tool requires python 2.7 (😱), but didn't pin all dependencies, so one of it (tabulate), is installed as a python3 tool, so has a broken syntax. The solution: fix the bioconda recipe by pinning all dependencies (or at least tabulate to tabulate=0.8.9)
Member
Author
There was a problem hiding this comment. I see. Just updated the Bioconda recipe, waiting for its approval |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,59 +1,45 @@ | ||
| process EKLIPSE { | ||
| tag "${meta.id}" | ||
| label 'process_single' | ||
|
|
||
| conda "${moduleDir}/environment.yml" | ||
| container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container | ||
| ? 'https://depot.galaxyproject.org/singularity/eklipse:1.8--hdfd78af_1' | ||
| : 'biocontainers/eklipse:1.8--hdfd78af_1'}" | ||
|
|
||
| input: | ||
| tuple val(meta), path(bam), path(bai) | ||
| path ref_gb | ||
|
|
||
| output: | ||
| tuple val(meta), path("*deletions.csv"), emit: deletions | ||
| tuple val(meta), path("*genes.csv"), emit: genes | ||
| tuple val(meta), path("*.png"), emit: circos | ||
| tuple val("${task.process}"), val('eklipse'), eval("eKLIPse.py 2>&1 | sed -n 's/.*\\[v\\([^]]*\\)\\].*/\\1/p' | tr '-' '.'"), emit: versions_eklipse, topic: versions | ||
|
|
||
| when: | ||
| task.ext.when == null || task.ext.when | ||
|
|
||
| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def ref_gb_path = ref_gb ? "${ref_gb}" : "/usr/local/bin/data/NC_012920.1.gb" | ||
| """ | ||
| echo "${bam}\t${prefix}" > infile.txt | ||
| eKLIPse.py \\ | ||
| -in infile.txt \\ | ||
| -ref ${ref_gb_path} \\ | ||
| ${args} | ||
| mv eKLIPse_*/eKLIPse_deletions.csv eKLIPse_${prefix}_deletions.csv | ||
| mv eKLIPse_*/eKLIPse_genes.csv eKLIPse_${prefix}_genes.csv | ||
| mv eKLIPse_*/eKLIPse_${prefix}.png eKLIPse_${prefix}.png | ||
| """ | ||
|
|
||
| stub: | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| touch eKLIPse_${prefix}_deletions.csv | ||
| touch eKLIPse_${prefix}_genes.csv | ||
| touch eKLIPse_${prefix}.png | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,11 +1,92 @@ | ||
| { | ||
| "homo_sapiens - bam": { | ||
| "content": [ | ||
| { | ||
| "circos": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "eKLIPse_test.png:md5,d1ea2a548bc4f8d321b1128a61ea8b0a" | ||
| ] | ||
| ], | ||
| "deletions": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "eKLIPse_test_deletions.csv:md5,8bcfdb8f3e8a63dcd211c2a53b6ca0a7" | ||
| ] | ||
| ], | ||
| "genes": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "eKLIPse_test_genes.csv:md5,ec1a1f31d018ca66a46d8a2d17bc8d18" | ||
| ] | ||
| ], | ||
| "versions_eklipse": [ | ||
| [ | ||
| "EKLIPSE", | ||
| "eklipse", | ||
| "1.8" | ||
| ] | ||
| ] | ||
| } | ||
| ], | ||
| "timestamp": "2026-04-14T21:32:53.481003", | ||
| "meta": { | ||
| "nf-test": "0.9.4", | ||
| "nextflow": "25.10.4" | ||
| } | ||
| }, | ||
| "homo_sapiens - bam - stub": { | ||
| "content": [ | ||
| { | ||
| "circos": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "eKLIPse_test.png:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "deletions": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "eKLIPse_test_deletions.csv:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "genes": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "eKLIPse_test_genes.csv:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "versions_eklipse": [ | ||
| [ | ||
| "EKLIPSE", | ||
| "eklipse", | ||
| "1.8" | ||
| ] | ||
| ] | ||
| } | ||
| ], | ||
| "timestamp": "2026-04-14T21:33:23.273542", | ||
| "meta": { | ||
| "nf-test": "0.9.4", | ||
| "nextflow": "25.10.4" | ||
| } | ||
| } | ||
| } |
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whoops