Add coptr module #6935
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Add coptr module #6935
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nvnieuwk
reviewed
Nov 14, 2024
Comment on lines
44
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45
| { assert snapshot(process.out.bam.collect{bam(it[1]).getReads(10)}).match() }, | ||
| { assert snapshot(process.out.bam.collect{bam(it[1]).getStatistics(include:["readCount"])}).match() } |
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Suggested change
| { assert snapshot(process.out.bam.collect{bam(it[1]).getReads(10)}).match() }, | |
| { assert snapshot(process.out.bam.collect{bam(it[1]).getStatistics(include:["readCount"])}).match() } | |
| { assert snapshot( | |
| process.out.bam.collect{bam(it[1]).getReads(10), | |
| process.out.bam.collect{bam(it[1]).getStatistics(include:"readCount"])} | |
| ).match() } |
This should fix your issue :) nf-test currently had no way to distinguish between both snapshot but my suggestion is the preferred way to fix this since we like to have one snapshot per test in nf-core
itrujnara
reviewed
Nov 19, 2024
| @@ -32,29 +32,7 @@ nextflow_process { | |||
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| } | |||
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| test("coptr index with multiple fastqs") { | |||
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What is the reason to remove this test?
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I changed something and the test broke, but I was going to address this in a separate PR as it's a different module
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OK, no problem. There might be some issues with tests as they are currently updating the CI workflow to use shards.
itrujnara
approved these changes
Nov 20, 2024
github-merge-queue bot
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Nov 20, 2024
* Initial addition * Updated snapshot * Updated snapshot * Updated tests. * Updated tests. * Updated snapshot * removed extra directory creation * Added plugin to only compare bam reads, not header * Added plugin to only compare bam reads, not header * Added plugin to only compare bam reads, not header * Output filename now also contains index id so as to not to repeat filenames * Updated snapshot * Updated snapshot * Added paired end test * Added paired end test * Updated tests to deal with bams changing order of reads each time * Updated tests to deal with bams changing order of reads each time * Updated tests to deal with bams changing order of reads each time * Updated tests to deal with bams changing order of reads each time * Updated container used * Added number of lines test for review * Added number of lines test for review * Updated nft-bam plugin * Updated container * Updated counting of reads * Updated counting of reads * removed * updated snapshot * Updated test and snapshot * Updated test and snapshot * fixed versions issue * fixed versions issue * fixed versions issue * fixed versions issue * fixed versions issue * fixed versions issue * Updated test * Updated test * Updated snapshot * Updated tag * Updated tests * Updated tests * Improved descriptions --------- Co-authored-by: James A. Fellows Yates <[email protected]> Co-authored-by: Igor Trujnara <[email protected]>
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PR checklist
Closes #XXX
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda