Add wipertools module (#7184) #7185
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
famosab
requested changes
Dec 10, 2024
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:true ], | ||
| file('https://raw.githubusercontent.com/nf-core/test-datasets/fastqrepair/testdata/truncated_clean.fastq', checkIfExists: true), |
famosab
reviewed
Dec 11, 2024
Comment on lines
+17
to
+29
| setup { | ||
| run("WIPERTOOLS_FASTQSCATTER") { | ||
| script "../../fastqscatter/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'pp_' ], // meta map | ||
| file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) | ||
| ] | ||
| input[1] = 2 // number of splits | ||
| """ | ||
| } | ||
| } |
There was a problem hiding this comment.
You could move the setup block before the first test block (line 12) and reuse it in all tests.
Comment on lines
+47
to
+48
| echo -e "@ERR001268.1 080821_HWI-EAS301_0002_30ALBAAXX:1:1:1090:1998/1" > ${out_folder}/${prefix}_1-of-2_suffix.fastq | ||
| echo -e "@ERR001268.2 080821_HWI-EAS301_0002_30ALBAAXX:1:1:1090:1998/2" > ${out_folder}/${prefix}_2-of-2_suffix.fastq |
There was a problem hiding this comment.
empty files suffice here :)
but if you get the number of chunks you could also reuse them in the output (so create more files for more chunks)
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
New module
PR checklist
Closes #7184
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile conda