Tetranscripts by hanalysis · Pull Request #9635 · nf-core/modules

hanalysis · 2026-01-10T14:38:30Z

PR checklist

Note - this module works as it currently is, but I could use some help adding something else. TEtranscripts usually works by searching in the same directory as the .bam files for a .bai file with the same naming convention. This is optional input (without the .bai, TEtranscripts just indexes the .bam files) which I understand would need to be passed through the same channels as the .bam files, and I haven't been able to get this to work. If anyone was happy to help me get this to work, I'd be very grateful, thanks!

itrujnara

Hi, thank you for the nice submission. There are some minor points for you to address. I have also left a suggestion about the index. Let me know if it works and if you need any further help.

modules/nf-core/tetranscripts/tests/main.nf.test

itrujnara · 2026-01-12T15:14:20Z

modules/nf-core/tetranscripts/meta.yml

+        pattern: "*.{bam}"
+
+        # Control BAM
+        ontologies: []


There should be ontologies for all the files, can you please find them? You can find a browser here

itrujnara · 2026-01-12T15:16:04Z

modules/nf-core/tetranscripts/main.nf

+        'biocontainers/tetranscripts:2.2.3--pyh7cba7a3_0' }"
+
+    input:
+    tuple val(meta_t), path(bam_t)


To add an optional index input, you should be able to simply extend these tuples. Nextflow does not have idiomatic optional arguments, but accepts [] as an empty value.

…into tetranscripts s q commit.

itrujnara

Thanks for the changes, it's almost ready now. You only need to add a test for the BAI input.

itrujnara · 2026-01-13T15:41:30Z

modules/nf-core/tetranscripts/tests/main.nf.test.snap

+        },
+        "timestamp": "2026-01-13T15:07:58.338450261"
+    },
+    "multiple files t - bam": {


I don't see any test where the BAM index is passed, can you please add one?

Thanks so much for such a quick review!

Just added the final commit - it turns out TEtranscripts doesn't actually use the BAM index files. I had thought this because it throws this error message in the log "[E::idx_find_and_load] Could not retrieve index file for '.1712579023.8525763.bam'", but it seems that this is an artefact from pysam and not relevant to TEtranscripts processes (see: mhammell-laboratory/TEtranscripts#185).

So, I've removed the .bai optional input, and added a test for the multiple .bams, hopefully this is everything addressed now! Thanks again.

itrujnara

Thanks for the changes, looks good now.

* adding tetranscripts module * Updating test files and correcting command typo * Successful singularity run test * Adding multiple files to test - wip * First effort to include multiple .bam * Multiple .bam processing add * Amending to test data * Add --sortByPos to config for test * Adding config to add parameters for test bams * Trying locally * Main working but stub failing with test data * Public data working main test and stub * Fixing linting! * Still linting * Linted and test passing public data - no .bai * Working Singularity * Remove TODO * Removed lingering TODO, linting 2 warnings, pass test * Changing main.nf to topics * Updating meta.yml to topics * Updating topics main.nf.test * Topics update linting pass test fail * Updated to topics passing linting and test * Fixing meta.yml typo - now passing linting and testing. * adding tetranscripts module * Updating test files and correcting command typo * Successful singularity run test * Adding multiple files to test - wip * First effort to include multiple .bam * Multiple .bam processing add * Amending to test data * Add --sortByPos to config for test * Adding config to add parameters for test bams * Trying locally * Main working but stub failing with test data * Public data working main test and stub * Fixing linting! * Still linting * Linted and test passing public data - no .bai * Working Singularity * Remove TODO * Removed lingering TODO, linting 2 warnings, pass test * Changing main.nf to topics * Updating meta.yml to topics * Updating topics main.nf.test * Topics update linting pass test fail * Updated to topics passing linting and test * Fixing meta.yml typo - now passing linting and testing. * Adding test for multiple bam files * adding ontologies to meta.yml * Adding .bai optional functionality * Adding optional .txt output channels * Removing bai input adding column test check for multiple files * Run prettier to fix pre-linting * Removing whitespace to pass prek * Adding back in additional lines end of file --------- Co-authored-by: Hannah Jones <hannah.18.jones@kcl.ac.uk> Co-authored-by: Hannah Jones <jonesh1@cn093.nemo.thecrick.org> Co-authored-by: Hannah Jones <jonesh1@cn092.nemo.thecrick.org> Co-authored-by: Hannah Jones <jonesh1@login006.nemo.thecrick.org> Co-authored-by: Hannah Jones <jonesh1@login007.nemo.thecrick.org>

Hannah Jones and others added 30 commits November 19, 2025 16:57

adding tetranscripts module

2fdcba5

Updating test files and correcting command typo

d07b869

Successful singularity run test

681c7ed

Adding multiple files to test - wip

718a444

First effort to include multiple .bam

51573d4

Multiple .bam processing add

1e120f3

Amending to test data

40215a3

Add --sortByPos to config for test

08062eb

Adding config to add parameters for test bams

6268b4c

Trying locally

4db3aa6

Main working but stub failing with test data

9966c64

Public data working main test and stub

fe4b5d6

Fixing linting!

8b5ba95

Still linting

1546e5f

Linted and test passing public data - no .bai

70cf2d3

Working Singularity

5e07e24

Remove TODO

2e1acfc

Removed lingering TODO, linting 2 warnings, pass test

9bc319a

Changing main.nf to topics

1775924

Updating meta.yml to topics

76b0b01

Updating topics main.nf.test

c068363

Topics update linting pass test fail

78216e2

Updated to topics passing linting and test

502d95f

Fixing meta.yml typo - now passing linting and testing.

c563b5b

adding tetranscripts module

b9a4e53

Updating test files and correcting command typo

7aeeed9

Successful singularity run test

d16a48d

Adding multiple files to test - wip

8ca293d

First effort to include multiple .bam

b077342

Multiple .bam processing add

ca23268

Hannah Jones and others added 9 commits January 10, 2026 14:23

Remove TODO

fdb7492

Removed lingering TODO, linting 2 warnings, pass test

8c1f3a6

Changing main.nf to topics

2d4aa49

Updating meta.yml to topics

37d57c5

Updating topics main.nf.test

e5a1fed

Topics update linting pass test fail

620d59b

Updated to topics passing linting and test

f8b81a6

Fixing meta.yml typo - now passing linting and testing.

a4f5295

Merge branch 'nf-core:master' into tetranscripts

0478893

itrujnara reviewed Jan 12, 2026

View reviewed changes

Hannah Jones and others added 5 commits January 13, 2026 12:51

Merge branch 'tetranscripts' of github.com:hanalysis/nf-core-modules …

7b1a8d2

…into tetranscripts s q commit.

Adding test for multiple bam files

29b6648

adding ontologies to meta.yml

dda863b

Adding .bai optional functionality

2618f98

Adding optional .txt output channels

4ffdfc4

itrujnara reviewed Jan 13, 2026

View reviewed changes

Removing bai input adding column test check for multiple files

f67602d

hanalysis requested a review from itrujnara January 14, 2026 10:37

Run prettier to fix pre-linting

e2dc82c

itrujnara approved these changes Jan 14, 2026

View reviewed changes

Merge branch 'master' into tetranscripts

123bdff

hanalysis enabled auto-merge January 14, 2026 15:27

hanalysis added 2 commits January 14, 2026 15:48

Removing whitespace to pass prek

6661809

Adding back in additional lines end of file

711abfe

hanalysis added this pull request to the merge queue Jan 14, 2026

Merged via the queue into nf-core:master with commit debd168 Jan 14, 2026
29 checks passed

hanalysis deleted the tetranscripts branch January 14, 2026 16:05

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Tetranscripts#9635

Tetranscripts#9635
hanalysis merged 59 commits intonf-core:masterfrom
hanalysis:tetranscripts

hanalysis commented Jan 10, 2026

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hanalysis commented Jan 10, 2026

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