sub-workflows dependencies are only displayed when uninstalling a workflow, not when installing it
Open
@xorrito624 is already working on this.
Since Jun 26, 2026.
bug
subworkflows
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
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
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Assessment
This issue has not been assessed yet.