8000 Linting of patched module fails · Issue #3540 · nf-core/tools · GitHub
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mashehu opened this issue Apr 17, 2025 · 1 comment
Open

Linting of patched module fails #3540

mashehu opened this issue Apr 17, 2025 · 1 comment
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bug Something isn't working linting

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@mashehu
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mashehu commented Apr 17, 2025 •
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Description of the bug

Adding an additional input to deeptools/bamcoverage (in meta.yml and main.nf) and running nf-core modules patch breaks linting.
My hunch is that the patch is not applied correctly, because if I remove the .diff file, linting is only complaining about the differences to the remote file, not any missing inputs.

Command used and terminal output

-core modules lint deeptools/bamcoverage
]

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.3.0.dev0 - https://nf-co.re


INFO     Linting pipeline: '.'
INFO     Linting module: 'deeptools/bamcoverage'

╭─ [!] 2 Module Test Warnings ──────────────────────────────────────────────────────────────────────────────────╮
│                        ╷                                          ╷                                           │
│ Module name            │ File path                                │ Test message                              │
│╶───────────────────────┼──────────────────────────────────────────┼──────────────────────────────────────────╴│
│ deeptools/bamcoverage  │ modules/nf-core/deeptools/bamcoverage/m… │ Conda update: bioconda::deeptools 3.5.5   │
│                        │                                          │ -> 3.5.6                                  │
│ deeptools/bamcoverage  │ modules/nf-core/deeptools/bamcoverage/m… │ Conda update: bioconda::samtools 1.20 ->  │
│                        │                                          │ 1.21                                      │
│                        ╵                                          ╵                                           │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ [✗] 2 Module Tests Failed ───────────────────────────────────────────────────────────────────────────────────╮
│                        ╷                                          ╷                                           │
│ Module name            │ File path                                │ Test message                              │
│╶───────────────────────┼──────────────────────────────────────────┼──────────────────────────────────────────╴│
│ deeptools/bamcoverage  │ modules/nf-core/deeptools/bamcoverage/m… │ Local copy of module does not match       │
│                        │                                          │ remote                                    │
│ deeptools/bamcoverage  │ modules/nf-core/deeptools/bamcoverage/m… │ Module meta.yml does not match main.nf.   │
│                        │                                          │ Inputs should contain: [['meta', 'input', │
│                        │                                          │ 'input_index'], ['fasta'], ['fasta_fai'], │
│                        │                                          │ ['blacklist']] Run nf-core modules lint   │
│                        │                                          │ --fix to update the meta.yml file.        │
│                        ╵                                          ╵                                           │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────╮

with the following diff file:

Changes in component 'nf-core/deeptools/bamcoverage'
'modules/nf-core/deeptools/bamcoverage/environment.yml' is unchanged
Changes in 'deeptools/bamcoverage/meta.yml':
--- modules/nf-core/deeptools/bamcoverage/meta.yml
+++ modules/nf-core/deeptools/bamcoverage/meta.yml
@@ -38,6 +38,9 @@
         type: file
         description: Index of the reference file (optional, but recommended)
         pattern: "*.{fai}"
+  - - blacklist:
+        type: file
+        description: Blacklist file
 output:
   - bigwig:
       - meta:

Changes in 'deeptools/bamcoverage/main.nf':
--- modules/nf-core/deeptools/bamcoverage/main.nf
+++ modules/nf-core/deeptools/bamcoverage/main.nf
@@ -1,6 +1,6 @@
 process DEEPTOOLS_BAMCOVERAGE {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -11,6 +11,7 @@
     tuple val(meta), path(input), path(input_index)
     path(fasta)
     path(fasta_fai)
+    path(blacklist)
 
     output:
     tuple val(meta), path("*.bigWig")   , emit: bigwig, optional: true
@@ -24,6 +25,7 @@
     def args      = task.ext.args ?: ''
     def prefix    = task.ext.prefix ?: "${meta.id}"
     def extension = args.contains("--outFileFormat bedgraph") || args.contains("-of bedgraph") ? "bedgraph" : "bigWig"
+    def blacklist_params = blacklist ? "--blackListFileName    st}" : ""
 
     // cram_input is currently not working with deeptools
     // therefore it's required to convert cram to bam first
@@ -39,6 +41,7 @@
         bamCoverage \\
             --bam $input_out \\
             $args \\
+            $blacklist_params \\
             --numberOfProcessors ${task.cpus} \\
             --outFileName ${prefix}.${extension}
 
@@ -54,6 +57,7 @@
         bamCoverage \\
             --bam $input_out \\
             $args \\
+            $blacklist_params \\
             --numberOfProcessors ${task.cpus} \\
             --outFileName ${prefix}.${extension}
 

'modules/nf-core/deeptools/bamcoverage/tests/main.nf.test.snap' is unchanged
'modules/nf-core/deeptools/bamcoverage/tests/main.nf.test' is unchanged
************************************************************

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@mashehu mashehu added bug Something isn't working linting labels Apr 17, 2025
@awgymer
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awgymer commented Apr 23, 2025 
# Check if we have a patch file, get original file in that case
meta_yaml_content = read_meta_yml(module_lint_object, module)

It seems like for the meta_yml lint test we actually explicitly seek the un-patched content. The issue is that then when a check on the channels from the main.nf is done this uses the code in the patched file (logic is in the nfcore_component.py)

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