Subworkflow update by DLBPointon · Pull Request #132 · sanger-tol/curationpretext

DLBPointon · 2026-02-06T22:43:49Z

#130 - FOFN or FILE input
#129 - Update to use Jim's Module

@prototaxites - Can you have a look at the implementation of your hic mapping subworkflow into curationpretext please?

I've replaced the current method and am using the below to test (otherwise it will die as i havn't replaced the pretext mapper bits yet:

nextflow run /lustre/scratch124/tol/teams/tola/users/dp24/curationpretext/main.nf -profile test,sanger,singularity --skip_tracks ALL

The test data is in the above dir. Essentially, processes are occasionally getting past here:

    ch_hic_cram_meta_mod = ch_hic_cram
        .transpose()
        .map { meta, cram -> [ meta + [ cramfile: cram ], cram ]}

But no further.

Input cram channel to the subworkflow is:

[[id:CurationPretextTest], [/lustre/scratch124/tol/teams/tola/users/dp24/curationpretext/TreeValTinyData/genomic_data/hic-arima/SUBSET-1000.cram, /lustre/scratch124/tol/teams/tola/users/dp24/curationpretext/TreeValTinyData/genomic_data/hic-arima/SUBSET-2000.cram]]

Pipeline will freeze like:

executor >  lsf (4)
[-        ] SANGER_TOL_CURATIONPRETEXT:CURATIONPRETEXT:GUNZIP                          -
[07/419b31] SAN…ATIONPRETEXT:CURATIONPRETEXT:GAWK_UPPER_SEQUENCE (CurationPretextTest) [100%] 1 of 1 ✔
[df/14942d] SAN…ETEXT:CURATIONPRETEXT:SAMTOOLS_FAIDX (CurationPretextTest_UPPER.fasta) [100%] 1 of 1 ✔
[-        ] SANGER_TOL_CURATIONPRETEXT:CURATIONPRETEXT:ALIGN_CRAM:SAMTOOLS_INDEX       -
[-        ] SAN…TOL_CURATIONPRETEXT:CURATIONPRETEXT:ALIGN_CRAM:CRAMALIGN_GENCRAMCHUNKS -
[-        ] SANGER_TOL_CURATIONPRETEXT:CURATIONPRETEXT:ALIGN_CRAM:SAMTOOLS_SPLITHEADER -
[04/3679f1] SAN…TIONPRETEXT:ALIGN_CRAM:BWAMEM2_INDEX (CurationPretextTest_UPPER.fasta) [100%] 1 of 1 ✔
[-        ] SAN…L_CURATIONPRETEXT:CURATIONPRETEXT:ALIGN_CRAM:CRAMALIGN_BWAMEM2ALIGNHIC -
[dd/4981dd] SAN…AMTOOLS_MERGE_MARKDUP:SAMTOOLS_FAIDX (CurationPretextTest_UPPER.fasta) [100%] 1 of 1 ✔
[-        ] SAN…URATIONPRETEXT:ALIGN_CRAM:BAM_SAMTOOLS_MERGE_MARKDUP:SAMTOOLS_MERGEDUP -

Then dies with no error:

ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details
-[sanger-tol/curationpretext] Pipeline completed with errors-

.nextflow.log shows nothing, presumably I'm passing in a dogey channel, but everything looks fine to me.

Thanks

Edit: This can wait till Monday so feel free to ignore!

github-actions · 2026-02-06T22:46:33Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 7d281fc

+| ✅ 185 tests passed       |+
#| ❔  32 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   3 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.6.0
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: assets/nf-core-curationpretext_logo_light.png
files_exist - File is ignored: docs/images/nf-core-curationpretext_logo_light.png
files_exist - File is ignored: docs/images/nf-core-curationpretext_logo_dark.png
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: CODE_OF_CONDUCT.md
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File does not exist: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/config.yml
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-curationpretext_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-curationpretext_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-curationpretext_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/curationpretext/curationpretext/.github/workflows/awstest.yml
multiqc_config - multiqc_config

❔ Tests fixed:

rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: conf/base.config
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-curationpretext_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowCurationpretext.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.split_telomere= false
nextflow_config - Config default value correct: params.cram_chunk_size= 10000
nextflow_config - Config default value correct: params.all_output= false
nextflow_config - Config default value correct: params.multi_mapping= 0.0
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
readme - README Nextflow minimum version badge matched config. Badge: 25.04.0, Config: 25.04.0
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: sanger_test_full.yml
actions_schema_validation - Workflow validation passed: sanger_test.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - SAMTOOLS_MERGE found in conf/base.config and Nextflow scripts.
base_config - SAMTOOLS_MERGEDUP found in conf/base.config and Nextflow scripts.
base_config - PRETEXT_GRAPH found in conf/base.config and Nextflow scripts.
base_config - BWAMEM2_INDEX found in conf/base.config and Nextflow scripts.
base_config - MINIMAP2_INDEX found in conf/base.config and Nextflow scripts.
base_config - GAP_LENGTH found in conf/base.config and Nextflow scripts.
base_config - GNU_SORT found in conf/base.config and Nextflow scripts.
base_config - BEDTOOLS_INTERSECT found in conf/base.config and Nextflow scripts.
base_config - TELOMERE_WINDOWS found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - PRETEXT_INGEST_SNDRD found in conf/modules.config and Nextflow scripts.
modules_config - PRETEXTSNAPSHOT found in conf/modules.config and Nextflow scripts.
modules_config - PRETEXTMAP found in conf/modules.config and Nextflow scripts.
modules_config - UCSC_BEDGRAPHTOBIGWIG found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_REPLACE_DOTS found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_RENAME_IDS found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_REFORMAT_INTERSECT found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_GAP_LENGTH found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_GENERATE_GENOME_FILE found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_UPPER_SEQUENCE found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_SPLIT_DIRECTIONS found in conf/modules.config and Nextflow scripts.
modules_config - GNU_SORT_A found in conf/modules.config and Nextflow scripts.
modules_config - GNU_SORT_B found in conf/modules.config and Nextflow scripts.
modules_config - GNU_SORT_C found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_MAKEWINDOWS found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_INTERSECT found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_MAP found in conf/modules.config and Nextflow scripts.
modules_config - SEQTK_CUTN found in conf/modules.config and Nextflow scripts.
modules_config - PRETEXT_INGEST_SNDRD found in conf/modules.config and Nextflow scripts.
modules_config - PRETEXT_INGEST_HIRES found in conf/modules.config and Nextflow scripts.
modules_config - PRETEXTSNAPSHOT found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - TELOMERE_WINDOWS found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.5.2
rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-02-27 11:44:15

prototaxites · 2026-02-10T18:08:55Z

Hi @DLBPointon, will take a look in depth tomorrow but just to double check - do the cram and the assembly channels share a meta? This is needed in order to ensure the joins within work.

DLBPointon · 2026-02-10T19:04:34Z

No problem, thanks.

And it does indeed now but still an issue, this is from inside the subworkflow.

prototaxites · 2026-02-11T09:06:53Z

This is very strange, I don't understand what is happening. It looks like nothing goes through that .transpose() block, but I cannot at all see why that would be.

prototaxites · 2026-02-11T09:15:28Z

I found the problem. .transpose() only works on channel objects, but your function fn_get_validated_channel does not actually return a channel, just a tuple.

I fixed it so that it returns a channel instead, and now mapping runs. You could alteratively revert that change and do:

channel.of(fn_get_validated_channel(...))

if you prefer.

DLBPointon · 2026-02-12T16:27:08Z

I found the problem. .transpose() only works on channel objects, but your function fn_get_validated_channel does not actually return a channel, just a tuple.

I fixed it so that it returns a channel instead, and now mapping runs. You could alteratively revert that change and do:
channel.of(fn_get_validated_channel(...))
if you prefer.

Absolute legend, thanks a ton Jim. Now onto adding pairs_create_contact_maps.

…or new modules

prototaxites

Couple of implementation thoughts!

subworkflows/local/utils_nfcore_curationpretext_pipeline/main.nf

workflows/curationpretext.nf

prototaxites

Looks good to me, one last comment about documentation

README.md

This reverts commit d35429f.

DLBPointon · 2026-03-02T11:03:30Z

Somhow managed to poison the PR

No matter what, I can't get it into a usable state. Once the branch is switched to, then it is poisoned and useless. Mind boggling issue.

Instead I spent saturday morning re-writting the PR before the family got up, otherwise I would have thought about it all weekend.

new PR is: #136

DLBPointon added 3 commits February 6, 2026 20:43

Update all

b0244cd

Merge branch 'dev' into subworkflow-update

dedbff9

Update all

74b6e81

DLBPointon changed the base branch from main to dev February 6, 2026 22:44

DLBPointon marked this pull request as draft February 6, 2026 22:44

sanger-tol deleted a comment from github-actions bot Feb 6, 2026

Update to ensure matching meta

ae31750

fix(functions): fn_get_validated_channel should return a channel

2455ec8

DLBPointon added 16 commits February 13, 2026 09:50

Adding pairs file for the mapping and snapshot of the mapped reads

75cfe5a

Update to add the mapping and snapshot

7e8d5cb

Modules included by sanger-tol subworkflow

8d7a447

Updating the conf for the new subworkflows

f3fd480

updates for the new modules

3dfbfff

Update on the modules

7765f50

Update Everything!

3f3cb47

Adding modules

8502ce7

Adding modules

2ccedd5

Update prettier linting

641a9ad

Linting

8feb38f

Update for linting

a4bdcd5

Update changelog

c172550

Better params use

758a5fc

Update Changelog

3bc9f2d

Forgot to change 1 params

e27aeb6

DLBPointon added 10 commits February 26, 2026 15:29

change pre_mapped to pre_mapped_bam

25a8ea1

change pre_mapped to pre_mapped_bam and remove cram from required

ec543ea

Update

b5d6fd8

change pre_mapped to pre_mapped_bam

5ff9cb0

Again changed the align_cram section to support mapped_reads

dcc014a

Added warnings for params and field for mapped reads

7b25e61

Add bam to file exclusion

7ecbd16

Update image

911e06e

Update all to remove quotes, support pre_mapped_bam and update conf f…

5828a83

…or new modules

Linting!

b3b765c

prototaxites reviewed Feb 27, 2026

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DLBPointon added 4 commits February 27, 2026 10:48

Update logic to kill pipeline if both pre_mapped and cram

751e695

Update based on comments

024cfde

Update expected values

6a78b7a

Change schema for the mapped bam file input

3f13976

prototaxites reviewed Feb 27, 2026

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workflows/curationpretext.nf Show resolved Hide resolved

Fix from PR

d35429f

prototaxites approved these changes Feb 27, 2026

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DLBPointon added 8 commits February 27, 2026 11:41

Update comment

7d281fc

Add sanger-tol gap_finder

a8eaba9

Update accessory file subworkflow to use sanger-tol subworkflow

ea681da

Update files

45e9761

Update to modules for gap_finder

4515561

Update for gap_finder

96c8cde

REVERT

e4196de

Revert the revert from the revert to fix the issue from gap_finder

aa8f9ec

This reverts commit d35429f.

DLBPointon closed this Mar 2, 2026

github-project-automation bot moved this from In progress to Done in WRAP team board Mar 2, 2026

DLBPointon moved this from Done to No Longer Planned in WRAP team board Mar 3, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️

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