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nf-core download doesn't work with latest NF syntax #1379

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drpatelh opened this issue Jan 7, 2022 · 1 comment
Closed

nf-core download doesn't work with latest NF syntax #1379

drpatelh opened this issue Jan 7, 2022 · 1 comment
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bug Something isn't working download nf-core download high-priority
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@drpatelh
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drpatelh commented Jan 7, 2022

Description of the bug

$ nf-core download    

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

    nf-core/tools version 2.2



Specify the name of a nf-core pipeline or a GitHub repository name (user/repo).
? Pipeline name: rnaseq
? Select release / branch: 3.5  [release]

In addition to the pipeline code, this tool can download software containers.
? Download software container images: singularity

If transferring the downloaded files to another system, it can be convenient to have everything compressed in a single file.
This is not recommended when downloading Singularity images, as it can take a long time and saves very little space.
? Choose compression type: none
INFO     Saving 'nf-core/rnaseq'                                                                                                                                       download.py:160
          Pipeline revision: '3.5'                                                                                                                                                    
          Pull containers: 'singularity'                                                                                                                                              
          Using $NXF_SINGULARITY_CACHEDIR': /home/harshil/containers/singularity                                                                                                      
          Output directory: 'nf-core-rnaseq-3.5'                                                                                                                                      
INFO     Downloading workflow files from GitHub                                                                                                                        download.py:163
INFO     Downloading centralised configs from GitHub                                                                                                                   download.py:167
INFO     Found 1 container                                                                                                                                             download.py:472
Pulling singularity images ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━   0% • 0/1 completed
${ workflow.containerEngine ==  Copying from cache to target directory ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
CRITICAL [Errno 2] No such file or directory: '/home/harshil/containers/singularity/${ workflow.containerEngine == .img'                                               download.py:182
(nf-core) ~/testing 

The regex in the nf-core download script will need to be updated (and to be backward compatible).

Command used and terminal output

Try running nf-core download to fetch Singularity containers for v3.5 of nf-core/rnaseq.

@drpatelh drpatelh added bug Something isn't working high-priority labels Jan 7, 2022
@drpatelh drpatelh added this to the 2.2.1 milestone Jan 7, 2022
@drpatelh
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Old syntax

    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0"
    } else {
        container "quay.io/biocontainers/fastqc:0.11.9--0"
    }

New syntax

    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
        'quay.io/biocontainers/fastqc:0.11.9--0' }"

The fix would have to work with both of these to be backwards compatibly.

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