From a557cfb7753aa3d560b58b4911dfa2cc32eca3ee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= Date: Mon, 12 Jan 2026 15:48:38 +0100 Subject: [PATCH 1/3] feat: remove demix module from rule core --- workflow/Snakefile | 1 + workflow/core.smk | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/Snakefile b/workflow/Snakefile index d51459d..50ad23f 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -16,6 +16,7 @@ configfile: "config/targets.yaml" include: "core.smk" include: "rules/context.smk" +include: "rules/demix.smk" include: "rules/report.smk" rule all: diff --git a/workflow/core.smk b/workflow/core.smk index 2938351..f109d8e 100644 --- a/workflow/core.smk +++ b/workflow/core.smk @@ -16,7 +16,6 @@ REPORT_DIR_TABLES = Path(OUTDIR/"report/tables") include: "rules/fetch.smk" include: "rules/fasta.smk" include: "rules/asr.smk" -include: "rules/demix.smk" include: "rules/vaf.smk" include: "rules/pangolin.smk" include: "rules/distances.smk" From e7c2fcf77e8d94191ffe8d7f9adf4f38371febf4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= Date: Mon, 12 Jan 2026 15:57:35 +0100 Subject: [PATCH 2/3] fix: add demix include call for tests --- .test/Snakefile | 1 + 1 file changed, 1 insertion(+) diff --git a/.test/Snakefile b/.test/Snakefile index d3ff278..e264947 100644 --- a/.test/Snakefile +++ b/.test/Snakefile @@ -12,6 +12,7 @@ __version__ = "1.3.0" # Rules include: "../workflow/core.smk" +include: "../workflow/rules/demix.smk" include: "../workflow/rules/context.smk" include: "../workflow/rules/report.smk" From 3ff9031ae01a7471770c8ed688b2fc9fa9aefce3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= Date: Mon, 12 Jan 2026 16:00:25 +0100 Subject: [PATCH 3/3] feat: remove pangolin module from rule core --- .test/Snakefile | 1 + workflow/Snakefile | 1 + workflow/core.smk | 1 - 3 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.test/Snakefile b/.test/Snakefile index e264947..a8dd4aa 100644 --- a/.test/Snakefile +++ b/.test/Snakefile @@ -14,6 +14,7 @@ __version__ = "1.3.0" include: "../workflow/core.smk" include: "../workflow/rules/demix.smk" include: "../workflow/rules/context.smk" +include: "../workflow/rules/pangolin.smk" include: "../workflow/rules/report.smk" rule all: diff --git a/workflow/Snakefile b/workflow/Snakefile index 50ad23f..ea984fd 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -17,6 +17,7 @@ configfile: "config/targets.yaml" include: "core.smk" include: "rules/context.smk" include: "rules/demix.smk" +include: "rules/pangolin.smk" include: "rules/report.smk" rule all: diff --git a/workflow/core.smk b/workflow/core.smk index f109d8e..2bfe396 100644 --- a/workflow/core.smk +++ b/workflow/core.smk @@ -17,6 +17,5 @@ include: "rules/fetch.smk" include: "rules/fasta.smk" include: "rules/asr.smk" include: "rules/vaf.smk" -include: "rules/pangolin.smk" include: "rules/distances.smk" include: "rules/evolution.smk"