sarek
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Add FASTQ_ALIGN_DNA subworkflow
PR checklist
- [ ] This comment contains a description of changes (with reason).
- [ ] 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/sarek 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>
). - [ ] 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).
nf-core lint
overall result: Passed :white_check_mark: :warning:
Posted for pipeline commit 7ea759c
+| ✅ 154 tests passed |+
#| ❔ 4 tests were ignored |#
!| ❗ 1 tests had warnings |!
:heavy_exclamation_mark: Test warnings:
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pipeline_todos - TODO string in
methods_description_template.yml
: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
:grey_question: Tests ignored:
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files_unchanged - File ignored due to lint config:
assets/nf-core-sarek_logo_light.png
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lib/NfcoreTemplate.groovy
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CODE_OF_CONDUCT.md
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LICENSE
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readme - README Nextflow minimum version badge matched config. Badge:
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readme - README Nextflow minimum version in Quick Start section matched config. README:
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- pipeline_name_conventions - Name adheres to nf-core convention
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- schema_lint - Schema lint passed
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- schema_params - Schema matched params returned from nextflow config
- actions_schema_validation - Workflow validation passed: ci.yml
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modules_json - Only installed modules found in
modules.json
- multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
- multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
- multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
- modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
Run details
- nf-core/tools version 2.6
- Run at
2022-10-14 17:39:13
For the moment, neither snapaligner nor bowtie2 can be used because I haven't add them in our params.aligner
cfr snapaligner It's able to handle both, but you can disable it with settings. Splitting fastq's is not an issue, but that's of course a bad idea if you want to use the included duplicate marking.
our current config looks like this
// -b- : Don't lock threads to cpu cores, improves performance when scheduling multiple jobs/node
// -sm 10 : Allow 10GB of memory for sorting threads
withName: SNAP_ALIGN {
cpus = { check_max( meta.tag && meta.tag == "WGS" ? 36 : 18 , "cpus" ) }
memory = { check_max( meta.tag && meta.tag == "WGS" ? 252.GB : 126.GB , "memory" ) }
ext.when = {params.aligner == "snapaligner"}
ext.args = {[
"-so",
"-b-",
"-sm 10",
meta.readgroup ? "-R \"@RG\\t" + meta.readgroup.collect{ "$it.key:$it.value" }.join("\\t") + "\"" : ""
].join(" ").trim()}
publishDir = [ enabled: false ]
}
For the moment, neither snapaligner nor bowtie2 can be used because I haven't add them in our params.aligner
Probably late to the party, but have to say not a big fan of having dead code in the pipeline, it makes the whole thing less readable imo. Maybe let's discuss this later today
For the moment, neither snapaligner nor bowtie2 can be used because I haven't add them in our params.aligner
Probably late to the party, but have to say not a big fan of having dead code in the pipeline, it makes the whole thing less readable imo. Maybe let's discuss this later today
Not dead code, but a placeholder for future features
Also, there's no index for snap in iGenomes! hint hint @FriederikeHanssen 😉 https://nfcore.slack.com/archives/CELEMAGC9/p1657108775156149
I can't see any aligner tests in the CI. Am I right?
I can't see any aligner tests in the CI. Am I right?
https://github.com/nf-core/sarek/actions/runs/3240467988/jobs/5311130371