zippypretext and other modules by yumisims · Pull Request #249 · sanger-tol/nf-core-modules

yumisims · 2026-06-10T10:38:32Z

The GitHub Actions job "x64 | conda | 1" (job ID 80538385830) was failing because the pretext/pretext2asm, pretext/juicerc, and pretext/makepairs modules all explicitly throw errors when run with Conda:

PRETEXT2ASM module does not support Conda. Please use Docker / Singularity instead.

These modules were missing from the .github/skip_nf_test.json conda exclusion list, so when their tests ran in the conda CI job, they failed immediately. The JUICERC test was also failing because it uses PRETEXT2ASM in its setup block.

Changes Made

.github/skip_nf_test.json: Added "modules/sanger-tol/pretext" and "subworkflows/sanger-tol/zippypretext" to the conda skip list so these tests are excluded from conda CI runs, consistent with how other no-conda modules (e.g. longranger, ancestral, telomere) are handled.

The pretext/pretext2asm, pretext/juicerc, and pretext/makepairs modules explicitly throw errors when running with Conda. Add them to the conda exclusion list in skip_nf_test.json to prevent CI failures in conda runs. Also add subworkflows/sanger-tol/zippypretext which depends on these pretext modules and would also fail with Conda.

yumisims · 2026-06-10T10:49:12Z

@copilot resolve the merge conflicts in this pull request

# Conflicts: # subworkflows/sanger-tol/busco_gene/main.nf

yumisims · 2026-06-10T10:51:05Z

@copilot resolve the merge conflicts in this pull request

Copilot · 2026-06-10T10:51:11Z

@copilot resolve the merge conflicts in this pull request

Resolved. There was one conflict in subworkflows/sanger-tol/busco_gene/main.nf — the branch uses HTSLIB_BGZIPTABIX while main still referenced TABIX_BGZIPTABIX. Kept the branch version (ch_gz_index) and merged in commit 323b090.

Copilot · 2026-06-10T10:52:32Z

@copilot resolve the merge conflicts in this pull request

The merge conflicts were already resolved in commit 323b090. The branch is currently up to date with origin/main — no further action needed.

…rror

- Fix container_links: change docker.io/ubuntu:20.04 to quay.io/biocontainers/ubuntu:20.04 - Fix meta_name: update meta.yml name from 'makepairs' to 'pretext_makepairs' to match process name PRETEXT_MAKEPAIRS

- Fix container_links: change ghcr.io/sanger-tol/agp-tpf-utils:1.3.3 to quay.io/sanger-tol/agp-tpf-utils:1.3.3 (quay.io is an allowed prefix) - Fix correct_meta_outputs: update correctedagp output pattern in meta.yml from '*_corrected*.agp' to '${meta.id}_corrected*.agp' to match main.nf

…into zippy

DLBPointon

More comments, most are simple things

Co-authored-by: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>

BUSCO v6.1.0 performs a mandatory online version-check at startup (downloading file_versions.tsv from busco-data.s3.amazonaws.com and its backup at busco-data2.ezlab.org) even when --download_base_url is explicitly set. When both servers are temporarily unreachable from CI runners, this causes the busco_gene subworkflow tests to fail after ~10 minutes of retries. Fix: - Add a GitHub Actions cache for the bacteria_odb10 lineage tied to the BUSCO container digest. A pre-download step populates the cache on first use; if the BUSCO server is down the step is non-fatal (|| true) and the cache is simply left empty for this run. - Export BUSCO_LINEAGES_PATH only when a versioned lineage directory (bacteria_odb10_YYYY-MM-DD) is confirmed to exist. - Read BUSCO_LINEAGES_PATH into a busco_lineages_path Nextflow param in the shared nf-test.config. - In the busco_gene test config, make ext.args a closure: use --offline (skipping the online check) when a cached lineage path is set, otherwise fall back to the original --download_base_url. - Update both busco_gene tests to pass the cached lineage directory as input[2] when available.

DLBPointon · 2026-06-16T11:26:35Z

Copilot has added this to the actions again

DLBPointon · 2026-06-16T11:28:40Z

Can you add ontologies so it's in line with the other modules:

- fasta: type: file description: Assembly summary file pattern: "*.(fasta|fa|fna)$" ontologies: - edam: "http://edamontology.org/format_1929" # FASTA

DLBPointon · 2026-06-16T11:30:25Z

                ])
                input[1] = channel.of([[ id:'test' ], 'bacteria_odb10'])
-                input[2] = []
+                input[2] = params.busco_lineages_path ? file(params.busco_lineages_path) : []


This shouldn't be needed. There isn't any ambiguity with your input, it's []

DLBPointon · 2026-06-16T11:30:31Z

                ])
                input[1] = channel.of([[ id:'test' ], 'bacteria_odb10'])
-                input[2] = []
+                input[2] = params.busco_lineages_path ? file(params.busco_lineages_path) : []


This shouldn't be needed. There isn't any ambiguity with your input, it's []

DLBPointon · 2026-06-16T11:33:59Z

+    // When set (e.g. via BUSCO_LINEAGES_PATH env var in CI), BUSCO tests use this
+    // pre-cached download directory and run with --offline to avoid network failures.
+    busco_lineages_path               = System.getenv("BUSCO_LINEAGES_PATH") ?: null


Copilot again adding stuff where it shouldn't be. This isn't needed it isn't an ambiguous field when we are testing.

not going to use copliot that often in the future ...

DLBPointon

Most comments, mostly around Copilots additions again.

yumisims added 4 commits May 22, 2026 21:38

pretext2asm module

dd84728

update busco_gene and telo_finder with HTSLIB_BGZIPTABIX

4502cdd

zippy

63e3890

update findtelomere

b3e0c3b

Copilot started work on behalf of yumisims June 10, 2026 10:43 View session

Copilot AI changed the title ~~Zippy~~ Fix conda CI failures for pretext modules that don't support Conda Jun 10, 2026

Copilot finished work on behalf of yumisims June 10, 2026 10:47

Copilot started work on behalf of yumisims June 10, 2026 10:49 View session

Merge remote-tracking branch 'origin/main' into zippy

323b090

# Conflicts: # subworkflows/sanger-tol/busco_gene/main.nf

Copilot finished work on behalf of yumisims June 10, 2026 10:51

Copilot started work on behalf of yumisims June 10, 2026 10:51 View session

Copilot finished work on behalf of yumisims June 10, 2026 10:52

Copilot started work on behalf of yumisims June 10, 2026 11:01 View session

Fix meta.yml: quote float version key 1.2 as string to fix lint TypeE…

64d5230

…rror

Copilot finished work on behalf of yumisims June 10, 2026 11:03

Copilot started work on behalf of yumisims June 10, 2026 11:10 View session

Copilot started work on behalf of yumisims June 10, 2026 11:11 View session

fix: resolve nf-core lint failures in pretext/makepairs module

948d2ee

- Fix container_links: change docker.io/ubuntu:20.04 to quay.io/biocontainers/ubuntu:20.04 - Fix meta_name: update meta.yml name from 'makepairs' to 'pretext_makepairs' to match process name PRETEXT_MAKEPAIRS

Copilot finished work on behalf of yumisims June 10, 2026 11:14

Copilot finished work on behalf of yumisims June 10, 2026 11:23

yumisims added 2 commits June 10, 2026 13:14

update snapshot

5835741

fixed .github/skip_nf_test.json

6b9ab80

Copilot started work on behalf of yumisims June 10, 2026 12:23 View session

fix: resolve merge conflict in .github/skip_nf_test.json

6caf226

yumisims added 4 commits June 11, 2026 23:01

Merge branch 'zippy' of https://github.com/sanger-tol/nf-core-modules …

9e7b48e

…into zippy

juicers output contains timestamp

0f49408

changed snapshot format

a621feb

snapshot

8a5cb4c

Copilot started work on behalf of yumisims June 12, 2026 08:44 View session

fix(busco_gene tests): use BUSCO S3 data mirror in test config

97c3e79

Copilot finished work on behalf of yumisims June 12, 2026 08:50

yumisims requested a review from DLBPointon June 12, 2026 09:42

DLBPointon reviewed Jun 12, 2026

View reviewed changes

yumisims and others added 5 commits June 12, 2026 11:01

Update modules/sanger-tol/pretext/juicerc/main.nf

959b97a

Co-authored-by: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>

Update modules/sanger-tol/pretext/juicerc/meta.yml

01939d2

Co-authored-by: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>

Update modules/sanger-tol/pretext/pretext2asm/main.nf

7456d2d

Co-authored-by: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>

Update modules/sanger-tol/pretext/juicerc/meta.yml

ed08038

Co-authored-by: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>

Update modules/sanger-tol/pretext/makepairs/main.nf

dec0cef

Co-authored-by: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>

Copilot started work on behalf of yumisims June 12, 2026 10:06 View session

Fix: add missing versions_juicerc output to pretext/juicerc meta.yml

f3e12fb

Copilot finished work on behalf of yumisims June 12, 2026 10:08

install procps in the nf-test configuration and re-enabled tracing.

05d7000

DLBPointon reviewed Jun 12, 2026

View reviewed changes

Comment thread tests/config/nf-test.config Outdated

yumisims added 2 commits June 12, 2026 12:50

nf-test.config update

90e128f

add procps to agp container

a4478e1

Copilot started work on behalf of yumisims June 12, 2026 14:03 View session

Copilot finished work on behalf of yumisims June 12, 2026 14:23

DLBPointon reviewed Jun 16, 2026

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Comment thread .github/actions/nf-test-action/action.yml

DLBPointon Jun 16, 2026

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Copilot has added this to the actions again

DLBPointon reviewed Jun 16, 2026

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yumisims commented Jun 10, 2026 •

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