Closed tillenglert closed 5 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit b2947e8
+| ✅ 178 tests passed |+
!| ❗ 6 tests had warnings |!
@skrakau I added your code review comments, but now I needed to implement another check for the parameter max_task_num
as using a value below the number of chosen alleles it will fail to due to a divide by zero error.
I originally wanted to add this check within the Nextflow logic e.g. utils subworkflow and general test before any task is executed but as the alleles may not be unique between rows and multiple alleles can be assigned per row I needed to use the alleles.tsv
file created by the check_samplesheet_and_create_tables
process. As I needed to read in another file I didn't want to obscure the process of checking too much and created a file within the process containing the number of alleles which is now used to throw an error within the Process_Input
subworkflow.
If you have suggestions to handle this error differently please let me know! Otherwise this PR is ready for review! 👍
I originally wanted to add this check within the Nextflow logic e.g. utils subworkflow and general test before any task is executed but as the alleles may not be unique between rows and multiple alleles can be assigned per row I needed to use the
alleles.tsv
file created by thecheck_samplesheet_and_create_tables
process. As I needed to read in another file I didn't want to obscure the process of checking too much and created a file within the process containing the number of alleles which is now used to throw an error within theProcess_Input
subworkflow.If you have suggestions to handle this error differently please let me know! Otherwise this PR is ready for review! 👍
Would it somehow be possible to avoid writing another file within check_samplesheet_and_create_tables
? For example, by just checking the number of alleles in alleles.tsv
directly within PROCESS_INPUT
, such as using the countLines
operaotr or similar?
Would it somehow be possible to avoid writing another file within check_samplesheet_and_create_tables? For example, by just checking the number of alleles in alleles.tsv directly within PROCESS_INPUT, such as using the countLines operaotr or similar?
Absolutely true and way cleaner than my solution! I adjusted it to use the already existing alleles.tsv
! Thank you!
I added a dynamic increase of the chunk sizes to set a limit to the generated
PREDICT_EPITOPES
processes. The default value formaximum_process_num
is 1000, which is adjusted to the CFC2.0 HPC Cluster of Tübingen.PR checklist
nf-core lint
).nf-test test main.nf.test -profile test,docker
).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).