nf-core / nf-core/tools

sub-workflows dependencies are only displayed when uninstalling a workflow, not when installing it

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#3,871 1 comment 0 reactions 1 assignee View on GitHub

@xorrito624 is already working on this.

Since Jun 26, 2026.

bug subworkflows
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Python
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2d 3h
Merged PRs (30d)
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Description

Description of the bug

This is just a display issue. Internally, the install/uninstall work correctly.
See this example sub-workflow that uses 3 nf-core samtools modules

Command used and terminal output
$ nf-core subworkflows --git-remote https://github.com/sanger-tol/nf-core-modules.git install bam_samtools_merge_markdup

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

   nf-core/tools version 3.4.1 - https://nf-co.re

INFO     Installing 'bam_samtools_merge_markdup'
INFO     Use the following statement to include this subworkflow:

 include { BAM_SAMTOOLS_MERGE_MARKDUP } from '../subworkflows/sanger-tol/bam_samtools_merge_markdup/main'

$ ls modules/nf-core/samtools/
faidx  markdup  merge

The sub-workflow and the three modules are installed.

$ nf-core subworkflows --git-remote https://github.com/sanger-tol/nf-core-modules.git remove bam_samtools_merge_markdup

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

nf-core/tools version 3.4.1 - https://nf-co.re

INFO     Removed files for 'samtools/faidx' and its dependencies 'samtools/faidx'.
INFO     Removed files for 'samtools/markdup' and its dependencies 'samtools/markdup'.
INFO     Removed files for 'samtools/merge' and its dependencies 'samtools/merge'.
INFO     Removed files for 'bam_samtools_merge_markdup' and its dependencies 'bam_samtools_merge_markdup, samtools_faidx, samtools_markdup, samtools_merge'.

It would be very clear if the module dependencies were displayed when installing the sub-workflow.

System information

No response

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