From 012cbbe7c4f7cc7f200562c41c5f7d9c133c9a1d Mon Sep 17 00:00:00 2001
From: Manavalan Gajapathy <manag@uab.edu>
Date: Thu, 11 Feb 2021 09:38:16 -0600
Subject: [PATCH] gets somalier working
---
.gitignore | 8 +------
configs/workflow.yaml | 4 ++--
workflow/Snakefile | 35 ++++++++++++++++++++++++++++-
workflow/rules/somalier.smk | 44 +++++++++++++++++++++----------------
4 files changed, 62 insertions(+), 29 deletions(-)
diff --git a/.gitignore b/.gitignore
index 5df7def..d5cdec7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -72,17 +72,11 @@ target/
.ipynb_checkpoints/
# exclude data from source control by default
-# data/
-variant_annotation/data/
+data/
#snakemake
.snakemake/
-
-# exclude test data used for development
-to_be_deleted/test_data/data/ref
-to_be_deleted/test_data/data/reads
-
#logs
logs/
diff --git a/configs/workflow.yaml b/configs/workflow.yaml
index 22d858b..c846ab9 100644
--- a/configs/workflow.yaml
+++ b/configs/workflow.yaml
@@ -1,6 +1,6 @@
-- somalier:
+somalier:
tool: "/data/project/worthey_lab/projects/experimental_pipelines/mana/tools/somalier/0.2.12/somalier"
sites: "/data/project/worthey_lab/projects/experimental_pipelines/mana/tools/somalier/0.2.12/sites/sites.hg38.vcf.gz"
labels_1kg: "/data/project/worthey_lab/projects/experimental_pipelines/mana/tools/somalier/0.2.12/ancestry/ancestry-labels-1kg.tsv"
- somalier_1kg: "/data/project/worthey_lab/projects/experimental_pipelines/mana/tools/somalier/0.2.12/ancestry/somalier_1kg/*.somalier"
+ somalier_1kg: "/data/project/worthey_lab/projects/experimental_pipelines/mana/tools/somalier/0.2.12/ancestry/1kg-somalier/"
ref: "/data/project/worthey_lab/datasets_central/human_reference_genome/processed/GRCh38/no_alt_rel20190408/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"
diff --git a/workflow/Snakefile b/workflow/Snakefile
index f7cae27..d593579 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -7,18 +7,51 @@ module load snakemake/5.9.1-foss-2018b-Python-3.6.6
snakemake -s workflow/Snakefile --use-conda -p
'''
from pathlib import Path
+import pandas as pd
WORKFLOW_PATH = Path(workflow.basedir).parent
-
configfile: WORKFLOW_PATH / "configs/workflow.yaml"
+
+def get_samples(fpath):
+
+ samples = ()
+ with open(fpath, 'r') as f_handle:
+ for line in f_handle:
+ sample = line.split(' ')[1]
+ samples += (sample,)
+
+ return samples
+
+
EXTERNAL_DIR = Path("data/external")
RAW_DIR = Path("data/raw")
INTERIM_DIR = Path("data/interim")
PROCESSED_DIR = Path("data/processed")
+PROJECTS_PATH = Path(f"/data/project/worthey_lab/projects/")
+# PROJECTS_PATH = Path(f"/data/project/worthey_lab/projects/{PROJECT}/analysis")
+PROJECT_NAME = "MuscDyst_SU_MAlexander"
+SAMPLES = get_samples(RAW_DIR / f"ped/{PROJECT_NAME}.ped")
+print (SAMPLES)
+
+############## MODULES ##############
+include: "rules/somalier.smk"
+#########################################
+
+
+############ CONSTRAINTS ############
+wildcard_constraints:
+ sample = '|'.join(SAMPLES),
+ project = PROJECT_NAME
+#########################################
+
rule all:
input:
+ expand(str(PROCESSED_DIR / "somalier/{project}/somalier.html"),
+ project=[PROJECT_NAME]),
+ expand(str(PROCESSED_DIR / "somalier/{project}/somalier.somalier-ancestry.html"),
+ project=[PROJECT_NAME]),
diff --git a/workflow/rules/somalier.smk b/workflow/rules/somalier.smk
index 8d162e2..fffa89d 100644
--- a/workflow/rules/somalier.smk
+++ b/workflow/rules/somalier.smk
@@ -1,20 +1,21 @@
rule extract:
input:
- # TODO
- vcf = ""
+ vcf = PROJECTS_PATH / "{project}" / "analysis" / "{sample}" / "vcf" / "{sample}.vcf.gz",
+ vcf_index = PROJECTS_PATH / "{project}" / "analysis" / "{sample}" / "vcf" / "{sample}.vcf.gz.tbi",
somalier_tool = config['somalier']['tool'],
sites = config['somalier']['sites'],
ref_genome = config['somalier']['ref'],
output:
- TODO
- # message:
+ INTERIM_DIR / "somalier_extract/{project}/{sample}.somalier"
+ message:
+ "Running somalier extract. Project: {wildcards.project}"
params:
- outdir = lambda wildcards, output: Path(output[[0]]).parent,
+ outdir = lambda wildcards, output: Path(output[0]).parent,
shell:
r"""
{input.somalier_tool} extract \
--sites {input.sites} \
- --fasta {input.ref} \
+ --fasta {input.ref_genome} \
--out-dir {params.outdir} \
{input.vcf}
"""
@@ -22,15 +23,17 @@ rule extract:
rule relate:
input:
- # TODO
- extracted = "",
- # ped = ""
+ extracted = expand(str(INTERIM_DIR / "somalier_extract/{{project}}/{sample}.somalier"),
+ sample=SAMPLES),
+ # ped = RAW_DIR / "ped" / "{project}.ped",
somalier_tool = config['somalier']['tool'],
output:
- TODO
- # message:
+ expand(str(PROCESSED_DIR / "somalier/{{project}}/somalier.{ext}"),
+ ext=['html', 'groups.tsv', 'pairs.tsv', 'samples.tsv']),
+ message:
+ "Running somalier relate. Project: {wildcards.project}"
params:
- outdir = lambda wildcards, output: Path(output[[0]]).parent,
+ outdir = lambda wildcards, output: Path(output[0]).parent,
shell:
r"""
{input.somalier_tool} relate \
@@ -38,25 +41,28 @@ rule relate:
--output-prefix {params.outdir}/somalier \
{input.extracted}
"""
- # --ped {input.ped} \
+ # --ped {input.ped} \
rule ancestry:
input:
- # TODO
- extracted=""
+ extracted = expand(str(INTERIM_DIR / "somalier_extract/{{project}}/{sample}.somalier"),
+ sample=SAMPLES),
somalier_tool = config['somalier']['tool'],
labels_1kg = config['somalier']['labels_1kg'],
- somalier_1kg = config['somalier']['somalier_1kg'],
+ somalier_1kg = directory(config['somalier']['somalier_1kg']),
output:
- # message:
+ expand(str(PROCESSED_DIR / "somalier/{{project}}/somalier.somalier-ancestry.{ext}"),
+ ext=['html', 'tsv']),
+ message:
+ "Running somalier ancestry. Project: {wildcards.project}"
params:
- outdir = lambda wildcards, output: Path(output[[0]]).parent,
+ outdir = lambda wildcards, output: Path(output[0]).parent,
shell:
r"""
{input.somalier_tool} ancestry \
--output-prefix {params.outdir}/somalier \
--labels {input.labels_1kg} \
- {input.somalier_1kg} ++ \
+ {input.somalier_1kg}*.somalier ++ \
{input.extracted}
"""
--
GitLab