From e35810dceadf3921d1f62b08e1423b0a3105afa8 Mon Sep 17 00:00:00 2001 From: Kiah McIntosh Date: Mon, 18 May 2026 12:54:01 +0000 Subject: [PATCH] Remove pychopper remnants [CW-7246] --- README.md | 5 ++--- docs/06_pipeline_overview.md | 4 ++-- docs/11_FAQ.md | 1 - nextflow.config | 7 ------- 4 files changed, 4 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index 77eac09..0696c51 100644 --- a/README.md +++ b/README.md @@ -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 directories: -+ `ingress_results//` contains prepared reads, read statistics, sample - metadata, and optional `pychopper` outputs for each sample ++ `ingress_results//` contains prepared reads, read statistics, and sample + metadata for each sample + `cohort/` contains the primary joint `bambu` transcriptome, count tables, alignments, and optional cohort `SQANTI3` outputs + `samples//` 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: -+ optional `pychopper` preprocessing outputs under `ingress_results//` + the joint cohort `bambu` transcriptome under `cohort/` + the per-sample `bambu` transcriptomes under `samples//` + optional `SQANTI3` results under cohort and per-sample directories diff --git a/docs/06_pipeline_overview.md b/docs/06_pipeline_overview.md index 5cde13e..3bf9347 100644 --- a/docs/06_pipeline_overview.md +++ b/docs/06_pipeline_overview.md @@ -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 directories: -+ `ingress_results//` contains prepared reads, read statistics, sample - metadata, and optional `pychopper` outputs for each sample ++ `ingress_results//` contains prepared reads, read statistics, and sample + metadata for each sample + `cohort/` contains the primary joint `bambu` transcriptome, count tables, alignments, and optional cohort `SQANTI3` outputs + `samples//` contains the independent per-sample `bambu` outputs and diff --git a/docs/11_FAQ.md b/docs/11_FAQ.md index e7bf26a..f02d60b 100644 --- a/docs/11_FAQ.md +++ b/docs/11_FAQ.md @@ -81,7 +81,6 @@ Yes. Use `--transcriptome_mode fixed_annotation` together with `--ref_genome`, Expect the report and output folder to emphasise: -+ optional `pychopper` preprocessing outputs under `ingress_results//` + the joint cohort `bambu` transcriptome under `cohort/` + the per-sample `bambu` transcriptomes under `samples//` + optional `SQANTI3` results under cohort and per-sample directories diff --git a/nextflow.config b/nextflow.config index 88c5500..8fd3c61 100644 --- a/nextflow.config +++ b/nextflow.config @@ -57,7 +57,6 @@ params { ] common_sha = "sha21d552f9910c575766e5d465fcb7b52fefda4b79" container_sha = "sha02e44f706d88fa29d8344b78479f187db7eec4ec" - pychopper_sha = "shaaaf20a5a0e76f9e18bad21af639a6b69e4a31a2f" sqanti_sha = "sha5bd775836492699e2537ebf846098eb117191d87" agent = null epi2me_instance = null @@ -82,9 +81,6 @@ process { withLabel:wf_transcriptomes { 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 { container = "ontresearch/wf-transcriptomes-sqanti:${params.wf.sqanti_sha}" } @@ -121,9 +117,6 @@ profiles { withLabel:wf_transcriptomes { container = "${params.aws_image_prefix}-wf-transcriptomes-core:${params.wf.container_sha}" } - withLabel:wf_transcriptomes_pychopper { - container = "${params.aws_image_prefix}-wf-transcriptomes:${params.wf.pychopper_sha}" - } withLabel:wf_transcriptomes_sqanti { container = "${params.aws_image_prefix}-wf-transcriptomes-sqanti:${params.wf.sqanti_sha}" }