kfukuta/wf-transcriptomes-v202
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Merge branch 'cw-7246' into 'dev'

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Remove pychopper remnants [CW-7246]

See merge request epi2melabs/workflows/wf-transcriptomes!268
This commit is contained in:
Kiah McIntosh 2026-05-18 12:54:01 +00:00
commit 5d4009d92b
4 changed files with 4 additions and 13 deletions
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5
README.md
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@ -277,8 +277,8 @@ The workflow's analysis is controlled by a user provided genome, annotation, and
The published outputs are organised around a small number of top-level The published outputs are organised around a small number of top-level
directories: directories:
+ `ingress_results/<alias>/` contains prepared reads, read statistics, sample + `ingress_results/<alias>/` contains prepared reads, read statistics, and sample
metadata, and optional `pychopper` outputs for each sample metadata for each sample
+ `cohort/` contains the primary joint `bambu` transcriptome, count tables, + `cohort/` contains the primary joint `bambu` transcriptome, count tables,
alignments, and optional cohort `SQANTI3` outputs alignments, and optional cohort `SQANTI3` outputs
+ `samples/<alias>/` contains the independent per-sample `bambu` outputs and + `samples/<alias>/` contains the independent per-sample `bambu` outputs and
@ -583,7 +583,6 @@ Yes. Use `--transcriptome_mode fixed_annotation` together with `--ref_genome`,
Expect the report and output folder to emphasise: Expect the report and output folder to emphasise:
+ optional `pychopper` preprocessing outputs under `ingress_results/<alias>/`
+ the joint cohort `bambu` transcriptome under `cohort/` + the joint cohort `bambu` transcriptome under `cohort/`
+ the per-sample `bambu` transcriptomes under `samples/<alias>/` + the per-sample `bambu` transcriptomes under `samples/<alias>/`
+ optional `SQANTI3` results under cohort and per-sample directories + optional `SQANTI3` results under cohort and per-sample directories

4
docs/06_pipeline_overview.md
View File

@ -122,8 +122,8 @@ The workflow's analysis is controlled by a user provided genome, annotation, and
The published outputs are organised around a small number of top-level The published outputs are organised around a small number of top-level
directories: directories:
+ `ingress_results/<alias>/` contains prepared reads, read statistics, sample + `ingress_results/<alias>/` contains prepared reads, read statistics, and sample
metadata, and optional `pychopper` outputs for each sample metadata for each sample
+ `cohort/` contains the primary joint `bambu` transcriptome, count tables, + `cohort/` contains the primary joint `bambu` transcriptome, count tables,
alignments, and optional cohort `SQANTI3` outputs alignments, and optional cohort `SQANTI3` outputs
+ `samples/<alias>/` contains the independent per-sample `bambu` outputs and + `samples/<alias>/` contains the independent per-sample `bambu` outputs and

1
docs/11_FAQ.md
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@ -81,7 +81,6 @@ Yes. Use `--transcriptome_mode fixed_annotation` together with `--ref_genome`,
Expect the report and output folder to emphasise: Expect the report and output folder to emphasise:
+ optional `pychopper` preprocessing outputs under `ingress_results/<alias>/`
+ the joint cohort `bambu` transcriptome under `cohort/` + the joint cohort `bambu` transcriptome under `cohort/`
+ the per-sample `bambu` transcriptomes under `samples/<alias>/` + the per-sample `bambu` transcriptomes under `samples/<alias>/`
+ optional `SQANTI3` results under cohort and per-sample directories + optional `SQANTI3` results under cohort and per-sample directories

7
nextflow.config
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@ -57,7 +57,6 @@ params {
] ]
common_sha = "sha21d552f9910c575766e5d465fcb7b52fefda4b79" common_sha = "sha21d552f9910c575766e5d465fcb7b52fefda4b79"
container_sha = "sha02e44f706d88fa29d8344b78479f187db7eec4ec" container_sha = "sha02e44f706d88fa29d8344b78479f187db7eec4ec"
pychopper_sha = "shaaaf20a5a0e76f9e18bad21af639a6b69e4a31a2f"
sqanti_sha = "sha5bd775836492699e2537ebf846098eb117191d87" sqanti_sha = "sha5bd775836492699e2537ebf846098eb117191d87"
agent = null agent = null
epi2me_instance = null epi2me_instance = null
@ -82,9 +81,6 @@ process {
withLabel:wf_transcriptomes { withLabel:wf_transcriptomes {
container = "ontresearch/wf-transcriptomes-core:${params.wf.container_sha}" container = "ontresearch/wf-transcriptomes-core:${params.wf.container_sha}"
} }
withLabel:wf_transcriptomes_pychopper {
container = "ontresearch/wf-transcriptomes:${params.wf.pychopper_sha}"
}
withLabel:wf_transcriptomes_sqanti { withLabel:wf_transcriptomes_sqanti {
container = "ontresearch/wf-transcriptomes-sqanti:${params.wf.sqanti_sha}" container = "ontresearch/wf-transcriptomes-sqanti:${params.wf.sqanti_sha}"
} }
@ -121,9 +117,6 @@ profiles {
withLabel:wf_transcriptomes { withLabel:wf_transcriptomes {
container = "${params.aws_image_prefix}-wf-transcriptomes-core:${params.wf.container_sha}" container = "${params.aws_image_prefix}-wf-transcriptomes-core:${params.wf.container_sha}"
} }
withLabel:wf_transcriptomes_pychopper {
container = "${params.aws_image_prefix}-wf-transcriptomes:${params.wf.pychopper_sha}"
}
withLabel:wf_transcriptomes_sqanti { withLabel:wf_transcriptomes_sqanti {
container = "${params.aws_image_prefix}-wf-transcriptomes-sqanti:${params.wf.sqanti_sha}" container = "${params.aws_image_prefix}-wf-transcriptomes-sqanti:${params.wf.sqanti_sha}"
} }