Update tasmanian-mismatch to 2.0.4 - #72
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will this be run in "methylation-mode" or no? |
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Ooops… I will fix this tomorrow. Thank you for the catch!!
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From: Laura Blum ***@***.***>
Date: Tuesday, September 1, 2026 at 3:24 PM
To: nebiolabs/EM-seq ***@***.***>
Cc: Erijman, Ariel ***@***.***>; Author ***@***.***>
Subject: Re: [nebiolabs/EM-seq] Update tasmanian-mismatch to 2.0.4 (PR #72)
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[https://avatars.githubusercontent.com/u/51452159?s=20&v=4]lnblum left a comment (nebiolabs/EM-seq#72)<#72 (comment)>
will this be run in "methylation-mode" or no?
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sounds good, otherwise looks fine!
This reverts commit d93555e.
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🟡 Changes recommended
There are correctness/clarity issues in the updated Tasmanian version pin/reporting and README typos (including a GRCh38/GRCh39 mismatch) that should be fixed before approval.
Once you've addressed the issues Copilot identified, you can request another Copilot review.
Pull request overview
This PR updates the EM-seq Nextflow pipeline to use a newer tasmanian-mismatch tool version and adjusts documentation and test snapshots to reflect the updated environment/tooling.
Changes:
- Updated the
tasmanianmodule to usetasmanian-mismatchdirectly (new CLI invocation) and pinned a newer conda package version. - Updated README reference-genome download links/wording and clarified how to handle
nextflow.preview.topicfor Nextflow v24. - Refreshed
nf-testsnapshots (includingnf-testversion metadata).
File summaries
| File | Description |
|---|---|
modules/tasmanian.nf |
Pins/uses tasmanian-mismatch and updates how Tasmanian stats are generated + version reporting output tuple. |
README.md |
Updates reference-genome links (adds CpG island annotations) and adjusts the Nextflow v24 upgrade note. |
main.nf |
Comments out nextflow.preview.topic by default and adds guidance for older Nextflow versions. |
tests/main.nf.test.snap |
Updates stored test snapshot output/metadata for the current test environment (nf-test version, ordering). |
Review details
- Files reviewed: 4/4 changed files
- Comments generated: 4
- Review effort level: Lite
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| tag { library } | ||
| publishDir "${params.outputDir}/stats/tasmanian" | ||
| conda "bioconda::samtools=1.22 bioconda::tasmanian-mismatch=1.0.9" | ||
| conda "bioconda::tasmanian-mismatch=2.0.3" |
| tuple val(library), path("${library}.tasmanian.csv"), emit: for_agg | ||
| tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -n 1 | sed \'s/^samtools //\''), topic: versions | ||
| tuple val("${task.process}"), val('tasmanian'), val('*should be* 1.0.9'), topic: versions | ||
| tuple val("${task.process}"), val('tasmanian-mismatch'), val('*should be* 2.0.3'), topic: versions |
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| - **T2T CHM13**: [T2T_chm13v2.0+ meth_controls](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/T2T_chm13v2.0%2Bmeth_controls.fa.gz) [CpG Islands](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/human_t2t_cpg_islands.gtf) | ||
| - **GRCh38**: [GRCh39 + meth controls](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/grch38_core%2Bmeth_controls.fa.gz) [CpG Islands](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/human_grch38_cpg_islands.gtf) | ||
| - **GRCm39**: [GRCm39 + meth_controls](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/grcm39%2Bmeth_controls.fa.gz) [CpG Islands](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/grcm39_cpg_islands.gtf) |
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| As of July, 2026, Nextflow v24 or older is not supported anymore. | ||
| If using Nextlfow version 24 is your only option, | ||
| please add `nextflow.preview.topic = true` as the top line in *main.nf* | ||
| please uncomment `nextflow.preview.topic = true` as the top line in *main.nf* |
Member
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superseded by #74 |
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