new module: PERBASE #7457

camlloyd · 2025-02-10T09:36:35Z

PR checklist

Closes #7456 by adding new module: PERBASE

camlloyd · 2025-02-10T09:37:50Z

NB: matching Singularity container is not available for latest version 0.10.2.
Perhaps downgrade all to 0.10.1.

EDIT: actually, it is available for 0.10.2, but it doesn't appear on biocontainers.pro

itrujnara

Very nice work, it's almost good to go, just a handful of small questions

modules/nf-core/perbase/main.nf

itrujnara · 2025-02-14T14:55:42Z

modules/nf-core/perbase/meta.yml

+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`


Please confirm that single_end is relevant here

This is from the nf-core module template, but I believe it's still relevant here.

Alright, thanks

itrujnara · 2025-02-15T11:11:15Z

I've merged master for you and all irrelevant CI issues are gone. There is still some nf-test linting issue, unfortunately I can't determine what's wrong.

camlloyd · 2025-02-15T11:42:21Z

I've merged master for you and all irrelevant CI issues are gone. There is still some nf-test linting issue, unfortunately I can't determine what's wrong.

╭─ [✗] 1 Module Test Failed ───────────────────────────────────────────────────╮
│              ╷                               ╷                               │
│ Module name  │ File path                     │ Test message                  │
│╶─────────────┼───────────────────────────────┼──────────────────────────────╴│
│ perbase      │ modules/nf-core/perbase/test… │ md5sum for empty file found:  │
│              │                               │ d41d8cd98f00b204e9800998ecf84 │
│              │                               │ 27e                           │
│              ╵                               ╵                               │
╰──────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────╮
│ LINT RESULTS SUMMARY  │
├───────────────────────┤
│ [✔]  45 Tests Passed  │
│ [!]   0 Test Warnings │
│ [✗]   1 Test Failed   │
╰───────────────────────╯
Error: Process completed with exit code 1.

test("homo_sapiens - illumina - cram") is failing because it is trying to read the following URI in the CRAM header:

UR:/home/AD/gmackenz/nf-core_test_datasets/test-datasets/data/genomics/homo_sapiens/illumina/cram/../../genome/chr21/sequence/genome.fasta

See .command.log

[E::easy_errno] Libcurl reported error 60 (SSL peer certificate or SSH remote key was not OK)
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/974dc7aec0b755b19f031418fdedf293": Input/output error
[E::fai_build3_core] Failed to open the file /home/AD/gmackenz/nf-core_test_datasets/test-datasets/data/genomics/homo_sapiens/illumina/cram/../../genome/chr21/sequence/genome.fasta : No such file or directory
[E::refs_load_fai] Failed to open reference file '/home/AD/gmackenz/nf-core_test_datasets/test-datasets/data/genomics/homo_sapiens/illumina/cram/../../genome/chr21/sequence/genome.fasta'
[W::cram_get_ref] Failed to populate reference for id 0
[E::cram_decode_slice] Unable to fetch reference #0:5011214-6457162

[E::cram_next_slice] Failure to decode slice
thread '<unnamed>' panicked at src/commands/base_depth.rs:252:32:
Extracted a pileup: BamPileup
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

Therefore the output test.tsv.gz is empty.
I'll look at adding a reference fasta input.

itrujnara

It looks very nice now, I've left a few mostly aesthetic remarks

itrujnara · 2025-02-17T10:03:05Z

modules/nf-core/perbase/main.nf

+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''


Harshil alignment here would be great

Should this be applied in the module template upstream?
https://github.com/nf-core/tools/blob/main/nf_core/module-template/main.nf

itrujnara · 2025-02-17T10:03:11Z

modules/nf-core/perbase/main.nf

+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"


Should this be applied in the module template upstream?
https://github.com/nf-core/tools/blob/main/nf_core/module-template/main.nf

Possibly, I need to discuss this with core

Thanks, I can look at opening a PR if needed.

itrujnara · 2025-02-17T10:03:25Z

modules/nf-core/perbase/meta.yml

+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`


Alright, thanks

itrujnara · 2025-02-17T10:04:02Z

modules/nf-core/perbase/meta.yml

+    - index:
+        type: file
+        description: BAI/CRAI file
+        pattern: "*.{bai,crai}"


Is there no suitable index format on EDAM?

There is for BAI: https://edamontology.github.io/edam-browser/#format_3327
CRAI is still to be added: edamontology/edamontology#835
It looks like there are more general index entries too.

Can you please add the best fit for each entry? It will make life easier for some people

I have added the ontology for BAI.

The parent Data index format sounded the most appropriate, but has the notRecommendedForAnnotation attribute as it is a placeholder concept, rather than a specific file format.

itrujnara

Nice work, good to go. I'll have a look into the module template about the alignment.

camlloyd · 2025-02-18T09:34:49Z

Thank you for being an excellent reviewer @itrujnara 🌟

camlloyd added 2 commits February 9, 2025 22:44

Add skeleton

ef44c51

Update perbase

6987875

camlloyd marked this pull request as draft February 10, 2025 09:46

camlloyd added 2 commits February 10, 2025 12:19

Update perbase

b2b4b25

Update perbase

ae3dc8d

itrujnara reviewed Feb 14, 2025

View reviewed changes

camlloyd and others added 2 commits February 14, 2025 16:13

Harshil Alignment

dab52a4

Merge branch 'master' into perbase

f6608c0

Update perbase

ad12a35

camlloyd marked this pull request as ready for review February 16, 2025 16:28

Add ontology

108ad36

itrujnara reviewed Feb 17, 2025

View reviewed changes

Add ontology

f656b93

itrujnara approved these changes Feb 18, 2025

View reviewed changes

camlloyd added this pull request to the merge queue Feb 18, 2025

Merged via the queue into nf-core:master with commit be5b197 Feb 18, 2025
67 checks passed

camlloyd deleted the perbase branch February 18, 2025 09:46

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

new module: PERBASE #7457

new module: PERBASE #7457

camlloyd commented Feb 10, 2025 •

edited

Loading

camlloyd commented Feb 10, 2025 •

edited

Loading

itrujnara left a comment

itrujnara Feb 14, 2025

camlloyd Feb 14, 2025

itrujnara Feb 17, 2025

itrujnara commented Feb 15, 2025

camlloyd commented Feb 15, 2025

itrujnara left a comment

itrujnara Feb 17, 2025

camlloyd Feb 17, 2025

itrujnara Feb 17, 2025

camlloyd Feb 17, 2025

itrujnara Feb 17, 2025

camlloyd Feb 17, 2025

itrujnara Feb 17, 2025

itrujnara Feb 17, 2025

camlloyd Feb 17, 2025

itrujnara Feb 17, 2025

camlloyd Feb 17, 2025

itrujnara left a comment

camlloyd commented Feb 18, 2025

new module: PERBASE #7457

new module: PERBASE #7457

Conversation

camlloyd commented Feb 10, 2025 • edited Loading

PR checklist

camlloyd commented Feb 10, 2025 • edited Loading

itrujnara left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

itrujnara commented Feb 15, 2025

camlloyd commented Feb 15, 2025

itrujnara left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

itrujnara left a comment

Choose a reason for hiding this comment

camlloyd commented Feb 18, 2025

camlloyd commented Feb 10, 2025 •

edited

Loading

camlloyd commented Feb 10, 2025 •

edited

Loading