feat: configurable basic layout (#90)

* feat: configurable basic layout

* fix: added missing layouting infor for github

Author: cmeesters

config/config.yaml

@@ -3,8 +3,25 @@ instructor:
   affiliation: "Institution Line"
   affiliation2: "2nd Institution line, if wanted" # may be empty
 
+layout:
+  beamertheme: "CambridgeUS" # you can choose any, the slides are tested
+                             # with 'CambridgeUS'
+  colortheme: "beaver"       # you can choose any, the slides are tested with
+                             # 'beaver'
+  # choose any preconfigured color or those from the preamble
+  beamercolor_structure:  "fg=UniRot" 
+  beamercolor_title:      "fg=UniRot"
+  beamercolor_title_head: "fg=UniRot"
+
+  beamercolor_block_title: "bg=UniRot!20,fg=darkred"
+  beamercolor_block_body:  "fg=black, bg=plightgrey2"
+
+  beamercolor_block_title_alerted: "fg=white,bg=UniRot"
+  beamercolor_block_title_example: "fg=white,bg=PineGreen!80"
+  
 course:
   date: "datestring" # maybe: "\today"
+  edition: "edition 4"
   # Editors recommendations are a matter of taste and technological
   # setups (e.g. on-demand setups). Hence, specify an editor-slide,
   #  here:

config/config_Mainz_NHR.yaml

@@ -2,6 +2,22 @@ instructor:
   name: "Dr. Christian Meesters"
   affiliation: "Johannes Gutenberg Universität Mainz"
   affiliation2: "NHR SüdWest" # may be empty
+  
+layout:
+  beamertheme: "CambridgeUS" # you can choose any, the slides are tested
+                             # with 'CambridgeUS'
+  colortheme: "beaver"       # you can choose any, the slides are tested with
+                             # 'beaver'
+  # choose any preconfigured color or those from the preamble
+  beamercolor_structure:  "fg=UniRot" 
+  beamercolor_title:      "fg=UniRot"
+  beamercolor_title_head: "fg=UniRot"
+
+  beamercolor_block_title: "bg=UniRot!20,fg=darkred"
+  beamercolor_block_body:  "fg=black, bg=plightgrey2"
+
+  beamercolor_block_title_alerted: "fg=white,bg=UniRot"
+  beamercolor_block_title_example: "fg=white,bg=PineGreen!80"
 
 course:
   date: "datestring" # maybe: "\today"
@@ -14,6 +30,9 @@ course:
   # a condarc file on a cluster, copy and adjust
   # for your cluster.
   condarcfile: "common/condarc_mogon.tex"
+  # We provide a common software stack to avoid long
+  # installation sessions.
+  softwarepath: "/lustre/project/m2\_jgu-ngstraining/software"
   # these are the path names to contain sample data
   # see the README for explanations.
   pathtosetup: "/lustre/project/m2\_jgu-ngstraining/workflows"

config/config_for_github.yaml

@@ -2,6 +2,22 @@ instructor:
   name: "N.N."
   affiliation: "Snakemake Teaching Alliance"
   affiliation2: "" # may be empty
+  
+layout:
+  beamertheme: "CambridgeUS" # you can choose any, the slides are tested
+                             # with 'CambridgeUS'
+  colortheme: "beaver"       # you can choose any, the slides are tested with
+                             # 'beaver'
+  # choose any preconfigured color or those from the preamble
+  beamercolor_structure:  "fg=UniRot" 
+  beamercolor_title:      "fg=UniRot"
+  beamercolor_title_head: "fg=UniRot"
+
+  beamercolor_block_title: "bg=UniRot!20,fg=darkred"
+  beamercolor_block_body:  "fg=black, bg=plightgrey2"
+
+  beamercolor_block_title_alerted: "fg=white,bg=UniRot"
+  beamercolor_block_title_example: "fg=white,bg=PineGreen!80"
 
 # The configuration for github needs valid file strings!
 

setup/README.txt setup_creators/README.txt

@@ -0,0 +1,68 @@
+configfile: "config/config.yaml"
+
+rule all:
+    input:
+        "plots/quals.svg",
+        "calls/all.vcf"
+
+
+def get_bwa_map_input_fastqs(wildcards):
+    return config["samples"][wildcards.sample]
+
+rule bwa_map:
+    input:
+        "data/genome.fa",
+        get_bwa_map_input_fastqs
+    output:
+        temp("mapped_reads/{sample}.bam")
+    params:
+        rg=config["bwa_map"]["rg"]
+    log: "logs/bwa_mem/{sample}.log"
+    threads: 8
+    shell:
+        "(bwa mem -R '{params.rg}' -t {threads} {input} | "
+        "samtools view -Sb - > {output}) 2> {log}"
+
+
+rule samtools_sort:
+    input:
+        "mapped_reads/{sample}.bam"
+    output:
+        temp("sorted_reads/{sample}.bam")
+    log: "logs/samtools_sort/{sample}.log"
+    shell:
+        "samtools sort -T sorted_reads/{wildcards.sample} "
+        "-O bam {input} > {output} 2> {log}"
+
+
+rule samtools_index:
+    input:
+        "sorted_reads/{sample}.bam"
+    output:
+        "sorted_reads/{sample}.bam.bai"
+    log: "logs/samtools_index/{sample}.log
+    shell:
+        "samtools index {input} &> {log}"
+
+
+rule bcftools_call:
+    input:
+        fa="data/genome.fa",
+        bam=expand("sorted_reads/{sample}.bam", sample=config["samples"]),
+        bai=expand("sorted_reads/{sample}.bam.bai", sample=config["samples"])
+    output:
+        "calls/all.vcf"
+    log: "logs/bcftools_call.log"
+    shell:
+        "(bcftools mpileup -f {input.fa} {input.bam} | "
+        "bcftools call -mv - > {output}) &> {log}"
+
+
+rule plot_quals:
+    input:
+        "calls/all.vcf"
+    output:
+        "plots/quals.svg"
+    log: "logs/plot_quals.log"
+    script:
+        "scripts/plot-quals.py"

setup/condarc_barnard setup_creators/condarc_barnard

@@ -0,0 +1,6 @@
+samples:
+  A: A.fastq
+  B: B.fastq
+
+bwa_map:
+  rg=r"@RG\tID:{sample}\tSM:{sample}"

setup/condarc_mogon setup_creators/condarc_mogon

@@ -0,0 +1,19 @@
+default-resources:
+  slurm_partition=barnard
+
+set-resources:
+    bwa_map:
+        runtime: 5 # real scenarios will take more
+        mem_mb_per_cpu: 1800
+
+    samtools_sort:
+        runtime: 5
+        mem_mb_per_cpu: 1800
+
+    samtools_index:
+        runtime: 5
+        mem_mb_per_cpu: 1800
+
+    bcftools_call:
+        runtime: 15
+        mem_mb_per_cpu: 1800

setup/copy_script_ZIH_Dresden.sh setup_creators/copy_script_ZIH_Dresden.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
+
+bash Miniforge3-Linux-x86_64.sh
+
+rm Miniforge3-Linux-x86_64.sh

setup/copy_script_mogonII.sh setup_creators/copy_script_mogonII.sh

@@ -37,8 +37,8 @@
 \definecolor{UrlColor}{rgb}{0,0.08,0.45}
 \definecolor{links}{rgb}{0,0,0}
 
-\usetheme{CambridgeUS} % Pittsburgh, CambridgeUS
-\usecolortheme{beaver} %wolverine | crane | beaver | seahorse
+\usetheme{<++layout.theme++>} % Pittsburgh, CambridgeUS
+\usecolortheme{<++layout.colortheme++>} %wolverine | crane | beaver | seahorse
 \useinnertheme{rounded} 
 \useoutertheme{default}
 \usefonttheme{default}
@@ -51,7 +51,7 @@
 % side margins
 \setbeamersize{text margin left=0.5cm, text margin right=0.5cm}
 
-\setbeamercolor{structure}{fg=UniRot}% to modify  immediately all palettes
+\setbeamercolor{structure}{<++layout.beamercolor_structure++>}% to modify  immediately all palettes
 \setbeamercolor{title}{fg=UniRot}
 \setbeamercolor{title in head/foot}{fg=UniRot}