From e7f814ab395451d08693ab9ba993ab63c82d1887 Mon Sep 17 00:00:00 2001
From: Zilong-Li <zimusen94@gmail.com>
Date: Thu, 18 Jul 2024 15:30:32 +0200
Subject: [PATCH] update readme

---
 README.md                 |  8 +++++++
 config/README.md          |  7 +++++++
 config/config.yaml        |  4 ++--
 workflow/envs/quilt.yaml  |  9 ++++----
 workflow/rules/common.smk | 44 ++++++++++++++++++---------------------
 5 files changed, 42 insertions(+), 30 deletions(-)

diff --git a/README.md b/README.md
index 384db5e..3c0b5d6 100644
--- a/README.md
+++ b/README.md
@@ -14,6 +14,14 @@ This workflow is for imputation using low coverage whole genome sequencing data
 - bcftools
 - [vcfppR](https://github.com/Zilong-Li/vcfppR)
 
+## Quick start
+
+```
+git clone https://github.com/Zilong-Li/lcWGS-imputation-workflow
+cd .test && ln -s ../workflow
+snakemake -j10 -n
+```
+
 ## Usage
 
 The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=Zilong-Li%2FlcWGS-imputation-workflow).
diff --git a/config/README.md b/config/README.md
index 69fb439..543ebbe 100644
--- a/config/README.md
+++ b/config/README.md
@@ -20,3 +20,10 @@ Modify the list of `refsize` in `config/config.yaml`. In default `refsize=[0]`,
 # Different scenario run
 
 Modify the variable `scenario` in `config/config.yaml` to decide what analyses to run.
+
+- `all` : run all comparisions across all programs and settings. requires `truth` to be configured.
+- `speed`: run only speed comparisons across all programs and settings. 
+- `quilt1`: run only `QUILT`.
+- `quilt2`: run only `QUILT2`, which is the default.
+- `glimpse1`: run only `GLIMPSE`.
+- `glimpse2`: run only `GLIMPSE2`.
diff --git a/config/config.yaml b/config/config.yaml
index d010679..329d637 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -14,8 +14,8 @@ refsize: [0]
 
 chroms: ['chr20']
 
-#'all', 'speed', 'accuracy', 'quilt','glimpse','quilt1', 'quilt2', 'glimpse1',  'glimpse2'
-scenario: 'all'
+#'all', 'speed', 'accuracy', 'quilt1', 'quilt2', 'glimpse1',  'glimpse2'
+scenario: 'quilt2'
 
 # global programs
 time: "/usr/bin/time"
diff --git a/workflow/envs/quilt.yaml b/workflow/envs/quilt.yaml
index 391000b..6cf80ac 100644
--- a/workflow/envs/quilt.yaml
+++ b/workflow/envs/quilt.yaml
@@ -1,6 +1,7 @@
 channels:
-  - bioconda
-  - conda-forge
+ - r
 dependencies:
-  - r-stitch =1.6.6
-  - r-quilt =1.0.3
+ - r=4.2.2
+ - r-stitch=1.7.0
+ - r-mspbwt=0.1.0
+ - r-quilt=2.0.0
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index 36b0a4d..b9cbd5a 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -44,8 +44,16 @@ def get_all_results():
         return get_refpanel_sites()
     elif RUN == "accuracy":
         return get_accuracy_panelsize_plots(), get_accuracy_depth_plots()
-    elif RUN == "F1":
-        return get_accuracy_f1_plots()
+    elif RUN == "speed":
+        return get_speed_all_plots()
+    elif RUN == "quilt1":
+        return get_quilt_regular_results()
+    elif RUN == "quilt2":
+        return get_quilt_mspbwt_results()
+    elif RUN == "glimpse1":
+        return get_glimpse_results()
+    elif RUN == "glimpse2":
+        return get_glimpse2_results()
     elif RUN == "V2":
         return (
             get_quilt_mspbwt_accuracy(),
@@ -53,34 +61,13 @@ def get_all_results():
             get_glimpse2_accuracy(),
             get_speed_glimpse2_plots(),
         )
-    elif RUN == "speed":
-        return get_speed_all_plots()
-    elif RUN == "test":
-        return get_quilt_accuracy()
-    elif RUN == "quilt":
+    elif RUN == "quilt_all":
         return (
             get_quilt_regular_accuracy(),
             get_speed_quilt_regular_plots(),
             get_quilt_mspbwt_accuracy(),
             get_speed_quilt_mspbwt_plots(),
         )
-    elif RUN == "fast":
-        return (
-            get_quilt_regular_accuracy(),
-            get_speed_quilt_regular_plots(),
-            get_quilt_mspbwt_accuracy(),
-            get_speed_quilt_mspbwt_plots(),
-            get_glimpse2_accuracy(),
-            get_speed_glimpse2_plots(),
-        )
-    elif RUN == "quilt1":
-        return get_quilt_regular_accuracy(), get_speed_quilt_regular_plots()
-    elif RUN == "quilt2":
-        return get_speed_quilt_mspbwt_plots()
-    elif RUN == "glimpse1":
-        return get_glimpse_accuracy(), get_speed_glimpse_plots()
-    elif RUN == "glimpse2":
-        return get_glimpse2_accuracy(), get_speed_glimpse2_plots()
     else:
         raise RuntimeError("this is an invalid scenario!")
 
@@ -238,6 +225,15 @@ def get_glimpse_results():
     )
 
 
+def get_glimpse2_results():
+    return expand(
+        rules.glimpse2_ligate.output,
+        chrom=config["chroms"],
+        size=config["refsize"],
+        depth=config["downsample"],
+    )
+
+
 def if_exclude_samples_in_refpanel(wildcards):
     if REFPANEL[wildcards.chrom].get("exclude_samples"):
         return REFPANEL[wildcards.chrom]["exclude_samples"]