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* Upgraded Dockerfile for CellRanger to 7.2.0 * Upgraded all modules to use 7.2.0 CellRanger * Update dockerfile accordingly * Update mkfastq * Update to use docker hub for the images * Update dockerfile for 8.0.0 release * Improved readme * Update all modules to use 8.0.0 container * Make litner happier * fix version info * delete environment.yml files since it breaks linting and tool has no conda package * remove pytest * updated cellranger/mkref to nf-test * remove mkref from pytest * removed pytests * update naming of tests * updated cellranger/count tests for new v8.0.0 ( new version produces different results, thus new md5sums ) * remove cellranger/mkfastq from pytest * port cellranger/mkfastq to nf-test * remove cellranger/mkgtf from pytests * Fix lint * port cellranger/mkgtf to nf-tests * Fix md5sum, so things can be ported over * Fix untar tag for mkfastq * Porting the tests over to nf-test * Update tags * remove from pytest * port cellranger/vdj to nf-tests * ported cellranger/mkvdjref to nf-tests * update tag * remove from pytest * ported cellranger/multi to nf-test * Fix vdj tests and linting * Fix lint + tests for multi cellranger * Skip conda tests for nf-test * Fix multi tests, fix linting for multi tests * Fix multi after all * Fix conda in nf-test.yml * You again, CR/multi! * Fixed it * main.nf.test aktualisieren Co-authored-by: Maxime U Garcia <[email protected]> * main.nf.test aktualisieren Co-authored-by: Maxime U Garcia <[email protected]> * Ditched configs that are not used at all * Add vdj proper tests * versions for multi * mkref tests improvement(s) * Adding in versions, too * Adjusting time limits to 4 hours for cellranger modules (2hrs cause break) * Pin to CPU= 2 * Fix to 5GB * Add note * remove process-specific nextflow configuration for cellranger count * also for mkref * Remove process resource configurations * fix syntax error * Add resource limits for mkref --------- Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Felipe Marques de Almeida <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> Co-authored-by: Gregor Sturm <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,91 @@ | ||
| // nf-core modules test cellranger/mkfastq | ||
| nextflow_process { | ||
|
|
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| name "Test Process CELLRANGER_MKFASTQ" | ||
| script "../main.nf" | ||
| config "./nextflow.config" | ||
| process "CELLRANGER_MKFASTQ" | ||
|
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||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "cellranger" | ||
| tag "cellranger/mkfastq" | ||
| tag "untar" | ||
|
|
||
| setup { | ||
| run("UNTAR") { | ||
| script "modules/nf-core/untar/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [], | ||
| file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-1.2.0.tar.gz", checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
| test("cellranger - tiny - simple") { | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = UNTAR.out.untar.map{ it[1] } | ||
| input[1] = file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-simple-1.2.0.csv", checkIfExists: true) | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| test("cellranger - tiny - illumina") { | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = UNTAR.out.untar.map{ it[1] } | ||
| input[1] = file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-samplesheet-1.2.0.csv", checkIfExists: true) | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
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| test("cellranger - tiny - simple - stub") { | ||
|
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| options "-stub" | ||
|
|
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| when { | ||
| process { | ||
| """ | ||
| input[0] = UNTAR.out.untar.map{ it[1] } | ||
| input[1] = file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-simple-1.2.0.csv", checkIfExists: true) | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| } |
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