Fix documentation issues by dialvarezs · Pull Request #987 · nf-core/mag

dialvarezs · 2026-03-04T15:35:19Z

PR checklist

nf-core-bot · 2026-03-04T15:35:59Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

jfy133

Just minor things, thanks @dialvarezs !

jfy133 · 2026-03-04T16:17:04Z

 Note, do not change number of CPUs with custom config files for the processes `spades`, `spadeshybrid` or `megahit` when specifying the parameters `--spades_fix_cpus`, `--spadeshybrid_fix_cpus` and `--megahit_fix_cpu_1` respectively.

-> **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden.
+> **NB:** We specify the full process name (for example `NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES`) in the config file because this takes priority over the short name (`METASPADES`) and allows existing configuration using the full process name to be correctly overridden.


I think this is from the template so be careful during template merges!

So docs gets also pushed on template updates? I have never seen a merge conflict on docs.

I went to check on sarek, and it doesn't have the references to STAR_ALIGN or PANGOLIN either: https://nf-co.re/sarek/3.8.1/docs/usage/#custom-configuration

So we should be fine I guess. But will keep an eye on this on template updates.

jfy133 · 2026-03-04T16:17:16Z

 ### Resource requests

-Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
+Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with one of the retryable error codes configured in `conf/base.config`, it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.


I think this is from the template so be careful during template merges!

jfy133 · 2026-03-04T16:17:35Z

 ### Updating containers (advanced users)

-The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`.
+The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration.


I think this is from the template so be careful during template merges!

jfy133 · 2026-03-04T16:17:44Z

-1. Check the default version used by the pipeline in the module file for [Pangolin](https://github.com/nf-core/viralrecon/blob/a85d5969f9025409e3618d6c280ef15ce417df65/modules/nf-core/software/pangolin/main.nf#L14-L19)
-2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags)
-3. Create the custom config accordingly:
+For example, to override the container used by the `METASPADES` process in `nf-core/mag`:


I think this is from the template so be careful during template merges!

jfy133 · 2026-03-04T16:18:07Z

@@ -369,8 +371,8 @@ The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementatio

  ```nextflow
  process {
-      withName: PANGOLIN {
-          container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0'
+      withName: METASPADES {
+          container = 'https://depot.galaxyproject.org/singularity/spades:<tag>'
      }
  }
  ```
@@ -379,13 +381,13 @@ The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementatio

  ```nextflow
  process {
-      withName: PANGOLIN {
-          conda = 'bioconda::pangolin=3.0.5'
+      withName: METASPADES {
+          conda = 'bioconda::spades=<version>'
      }
  }
  ```

-> **NB:** If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the `work/` directory otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch.
+> **NB:** If you wish to periodically update individual tool-specific results generated by the pipeline, you must ensure to keep the `work/` directory, otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch.


I think all of this is from the template so be careful during template merges!

Co-authored-by: James A. Fellows Yates <[email protected]>

dialvarezs added 14 commits March 4, 2026 11:35

Fix naming of bin_*_size parameters

c1b97e1

Fix naming of save_checkm_data parameter

e3c07a2

Fix run_checkm parameter

9c00d80

Fix skip_ancient_damagecorrection parameter

822a020

Fix output paths

d7161b7

Remove raw read taxonomic classification from output overview

2c88841

Fix minimap2 host align output path

0cf49b9

Fix schema helps

4662a23

Clarify requirement of group in assembly_input

c1a34c8

Fix pydamage and adna variants outputs

04dcdd5

Update GTDB docs to match current default (r226)

b7de254

Update resources and custom tool args docs to make them related to mag

4c81383

Fix typos

c5732a9

Merge remote-tracking branch 'upstream/dev' into fix-docs

2e0ddea

dialvarezs requested review from d4straub, jfy133, muabnezor and prototaxites as code owners March 4, 2026 15:35

Update changelog

b09c2d7

dialvarezs changed the title ~~Fix several docs issues~~ Fix documentation issues Mar 4, 2026

jfy133 approved these changes Mar 4, 2026

View reviewed changes

Update CHANGELOG.md

eca6135

Co-authored-by: James A. Fellows Yates <[email protected]>

dialvarezs merged commit 0e39a92 into nf-core:dev Mar 5, 2026
40 of 42 checks passed

dialvarezs mentioned this pull request Mar 7, 2026

Release 5.4.1 #991

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Fix documentation issues#987

Fix documentation issues#987
dialvarezs merged 16 commits intonf-core:devfrom
dialvarezs:fix-docs

dialvarezs commented Mar 4, 2026

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dialvarezs Mar 5, 2026 •

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dialvarezs commented Mar 4, 2026

PR checklist

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dialvarezs Mar 5, 2026 •

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