While checking the pipeline again especially downstream analysis, I realised only one of the chosen alleles is used in plotting, instead of all. The reason was the input structures of the processes: PLOT_ENTITY_BINDING_RATIOS and PLOT_SCORE_DISTRIBUTION. They both had two single item inputs: path alleles and path conditions alongside the multi item input: path(prep_scores) which contains one file for each allele. I'm not quite sure what change broke the process, but it is only executed once (as intended by nextflow). Therefore adding an each to the multi item input fixes the behaviour.
PR checklist
[x] This comment contains a description of changes (with reason).
[x] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] If necessary, also make a PR on the nf-core/metapep branch on the nf-core/test-datasets repository.
[ ] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[ ] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).
While checking the pipeline again especially downstream analysis, I realised only one of the chosen alleles is used in plotting, instead of all. The reason was the input structures of the processes:
PLOT_ENTITY_BINDING_RATIOS
andPLOT_SCORE_DISTRIBUTION
. They both had two single item inputs:path alleles
andpath conditions
alongside the multi item input:path(prep_scores)
which contains one file for each allele. I'm not quite sure what change broke the process, but it is only executed once (as intended by nextflow). Therefore adding aneach
to the multi item input fixes the behaviour.PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).