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Merge pull request #11 from snakemake/fix/Dresden
fix: dresden
2 parents 816b332 + 297dfca commit f754fc8

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‎config/config_dresden.yaml

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@@ -2,9 +2,28 @@ instructor:
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name: "Dr. Christian Meesters"
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affiliation: "Johannes Gutenberg Universität Mainz"
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affiliation2: "NHR SüdWest" # may be empty
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layout:
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beamertheme: "CambridgeUS" # you can choose any, the slides are tested
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# with 'CambridgeUS'
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colortheme: "beaver" # you can choose any, the slides are tested with
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# 'beaver'
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# choose any preconfigured color or those from the preamble
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beamercolor_structure: "fg=UniRot"
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beamercolor_title: "fg=UniRot"
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beamercolor_title_head: "fg=UniRot"
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beamercolor_block_title: "bg=UniRot!20,fg=darkred"
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beamercolor_block_body: "fg=black, bg=plightgrey2"
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beamercolor_block_title_alerted: "fg=white,bg=UniRot"
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beamercolor_block_title_example: "fg=white,bg=PineGreen!80"
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course:
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date: "18. April 2024" # maybe: "\today"
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# sets the slides aspectratio (if outcommented, the default is 43=4:3)
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aspectratio: 1609 # - 169 = 16:9
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date: "26.-27. February 2025" # maybe: "\today"
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#title: "" # specifiy your title here, else a default is used.
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#subtitle: "" # specifiy your subtitle here, else a default is used.
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# Editors recommendations are a matter of taste and technological
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# a condarc file on a cluster, copy and adjust
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# for your cluster.
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condarcfile: "common/condarc_barnard.tex"
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# We provide a common software stack to avoid long
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# installation sessions.
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softwarepath: "/projects/p_nhr_snakemake/software_stack"
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# these are the path names to contain sample data
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# see the README for explanations.
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pathtosetup: "/projects/p_nhr_snakemake"
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pathtosolutions: "solutions"
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# This is the selected slide to explain the 'Hello World' script
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pathtosetup: "/projects/p_nhr_snakemake/tutorial"
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pathtosolutions: "/projects/p_nhr_snakemake/solutions"
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# after copying the setup path is:
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tutorialpath: "~/tasks"
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deploy_url: "https://github.com/snakemake-workflows/rna-seq-kallisto-sleuth"
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# This is the selected slide to explain the 'Hello World' script
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# to introduce SLURM. It requires different account and partition
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# settings on every cluster.
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hello_world_script: "common/Hello_World_HPC_Barnard.tex"
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cluster:
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# the cluster name
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name: "Barnard"
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# the cluster distro
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distro: "RedHat"
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# the cluster account and default partition
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#account: "m2_jgu-ngstraining"
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#account: "p_nhr_snakemake"
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partition: "barnard"
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# the local and remote storage prefixes on this cluster
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remotejoblocalstorageprefix: "/dev/shm/$USER/snakemake"

‎images/humor/up_to_date.jpg

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‎images/misc/bricks.png

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‎setup_creators/copy_script_ZIH_Dresden.sh

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@@ -2,15 +2,15 @@
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# This script is used to teach on the cluster "Mogon II"
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CLUSTER_ALIAS="nhr410@login1.barnard.hpc.tu-dresden.de"
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CLUSTER_ALIAS="barnard"
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BASEPATH="/projects/p_nhr_snakemake"
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# creating remote directory:
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ssh ${CLUSTER_ALIAS} "mkdir -p ${BASEPATH}"
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scp condarc_barnard "${CLUSTER_ALIAS}:${BASEPATH}/condarc"
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scp get_tutorial.sh "${CLUSTER_ALIAS}:${BASEPATH}/get_tutorial.sh"
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scp install_mamba.sh "${CLUSTER_ALIAS}:${BASEPATH}/install_mamba.sh"
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scp install_conda.sh "${CLUSTER_ALIAS}:${BASEPATH}/install_conda.sh"
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scp environment.yaml "${CLUSTER_ALIAS}:${BASEPATH}/environment.yaml"
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rsync -rtlv --chmod=D755 "tutorial" "${CLUSTER_ALIAS}:${BASEPATH}"

‎setup_creators/solutions/05_Snakefile_target

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# our samples are pre-configured
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SAMPLES = ["A", "B"]
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samples = ["A", "B"]
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rule all:
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input:
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rule bcftools_call:
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input:
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fa="data/genome.fa",
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bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
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bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
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bam=expand("sorted_reads/{sample}.bam", sample=samples),
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bai=expand("sorted_reads/{sample}.bam.bai", sample=samples)
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output:
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"calls/all.vcf"
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shell:

‎setup_creators/solutions/06_Snakefile_run

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# our samples are pre-configured
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SAMPLES = ["A", "B"]
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samples = ["A", "B"]
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rule all:
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input:
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rule bcftools_call:
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input:
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fa="data/genome.fa",
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bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
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bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
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bam=expand("sorted_reads/{sample}.bam", sample=samples),
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bai=expand("sorted_reads/{sample}.bam.bai", sample=samples)
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output:
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"calls/all.vcf"
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shell:

‎setup_creators/solutions/07_Snakefile_script

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# our samples are pre-configured
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SAMPLES = ["A", "B"]
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samples = ["A", "B"]
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rule all:
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rule bcftools_call:
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input:
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fa="data/genome.fa",
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bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
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bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
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bam=expand("sorted_reads/{sample}.bam", sample=samples),
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bai=expand("sorted_reads/{sample}.bam.bai", sample=samples)
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output:
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"calls/all.vcf"
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shell:

‎setup_creators/solutions/08_Snakefile_script2

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# our samples are pre-configured
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SAMPLES = ["A", "B"]
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samples = ["A", "B"]
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configfile: "config/config.yaml"
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rule bcftools_call:
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input:
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fa="data/genome.fa",
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bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
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bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
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bam=expand("sorted_reads/{sample}.bam", sample=samples),
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bai=expand("sorted_reads/{sample}.bam.bai", sample=samples)
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output:
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"calls/all.vcf"
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shell:

‎setup_creators/solutions/09_Snakefile_config

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# our samples are pre-configured
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SAMPLES = ["A", "B"]
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samples = ["A", "B"]
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configfile: "config/config.yaml"
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rule bcftools_call:
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input:
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fa="data/genome.fa",
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bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
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bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
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bam=expand("sorted_reads/{sample}.bam", sample=samples),
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bai=expand("sorted_reads/{sample}.bam.bai", sample=samples)
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output:
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"calls/all.vcf"
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shell:

‎setup_creators/solutions/13_Snakemake_wrapper

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configfile: "config/config.yaml"
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rule all:
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input:
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"calls/all.vcf",
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"calls/positions.png",
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"calls/quals.svg",
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def get_bwa_map_input_fastqs(wildcards):
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return config["samples"][wildcards.sample]
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rule bwa_mem:
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input:
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reads=get_bwa_map_input_fastqs,
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idx=multiext("data/genome.fa", ".amb", ".ann", ".pac", ".sa"),
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output:
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"sorted_reads/{sample}.bam",
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log:
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"logs/bwa_mem/{sample}.log",
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params:
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extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
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sorting="samtools", # Can be 'none', 'samtools' or 'picard'.
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sort_order="coordinate", # Can be 'queryname' or 'coordinate'.
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sort_extra="", # Extra args for samtools/picard.
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threads: 8
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wrapper:
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"v5.7.0/bio/bwa/mem"
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rule samtools_index:
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input:
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"sorted_reads/{sample}.bam",
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output:
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"sorted_reads/{sample}.bam.bai",
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log:
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"logs/samtools_index/{sample}.log",
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params:
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extra="", # optional params string
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threads: 4 # This value - 1 will be sent to -@
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wrapper:
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"v5.7.0/bio/samtools/index"
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rule bcftools_call:
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input:
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fa="data/genome.fa",
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bam=expand("sorted_reads/{sample}.bam", sample=config["samples"]),
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bai=expand("sorted_reads/{sample}.bam.bai", sample=config["samples"]),
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output:
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"calls/all.vcf",
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log:
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"logs/bcftools_call/bcftools.log",
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shell:
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"(bcftools mpileup -f {input.fa} {input.bam} | "
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"bcftools call -mv - > {output}) 2> {log}"
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rule plot_positions:
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input:
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rules.bcftools_call.output,
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output:
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"calls/positions.png",
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script:
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"scripts/plot-positions.py"
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rule plot_quals:
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input:
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"calls/all.vcf",
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output:
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"calls/quals.svg",
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script:
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"scripts/plot-quals.py"

‎setup_creators/tutorial/05_Snakefile_target

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# our samples are pre-configured
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SAMPLES = ["A", "B"]
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samples = ["A", "B"]
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#TASK: Figure out, which your final target is.
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# This is the final target of our workflow, so far.
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rule bcftools_call:
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input:
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fa="data/genome.fa",
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bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
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bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
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bam=expand("sorted_reads/{sample}.bam", sample=samples),
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bai=expand("sorted_reads/{sample}.bam.bai", sample=samples)
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output:
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"calls/all.vcf"
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shell:

‎setup_creators/tutorial/06_Snakefile_run

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# our samples are pre-configured
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SAMPLES = ["A", "B"]
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samples = ["A", "B"]
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#TASKS: This is an almost working Snakefile!
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# But it is scrambled and contains a bug.
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rule bcftools_call:
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input:
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fa="data/genome.fa",
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bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
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bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
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bam=expand("sorted_reads/{sample}.bam", sample=samples),
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bai=expand("sorted_reads/{sample}.bam.bai", sample=samples)
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output:
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"calls/all.vcf"
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shell:

‎slides/Snakemake_HPC_User_Creator_Combi.tex

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\include{common/HPC_101}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\include{users/Selecting_Workflows}
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\include{creators/Selecting_Workflows}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\include{creators/Getting_Started}
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\include{common/Reports}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\include{common/using_wrappers}
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\include{creators/using_wrappers}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\include{creators/modularization}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\include{common/Contributing}

‎slides/common/HPC_101.tex

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% source: https://en.m.wikipedia.org/wiki/File:Text-x-python.svg
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}
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\frame{
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\frametitle{Using Code-Studio}
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\frametitle{Running ordinary Batch Scripts}
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\begin{mdframed}[tikzsetting={draw=white,fill=white,fill opacity=0.8,
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line width=0pt},backgroundcolor=none,leftmargin=0,
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rightmargin=150,innertopmargin=4pt,roundcorner=10pt]

‎slides/common/InTouch.tex

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\frametitle{Mastodon Announcement Bot II}
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\begin{columns}
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\begin{column}{0.5\textwidth}
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\includegraphics[width=0.8\textwidth]{contact/announcement_robot_example_screenshot.png}\\
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\includegraphics[width=0.8\textwidth]{contact/announcement_robot_example_sreenshot.png}\\
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Screenshot from Mastodon
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\end{column}
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\begin{column}{0.5\textwidth}

‎slides/common/contributions.tex

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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\begin{frame}
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\frametitle{Honour where Honour is due}
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The current \Snakemake HPC Teaching Alliance contributors:
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\begin{columns}
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\begin{column}{.5\textwidth}
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\begin{itemize}
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\end{itemize}
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\end{column}
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\end{columns}
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\vfill
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The concept article is published in \lhref{https://doi.org/10.14279/eceasst.v83.2600}{the "Electronic Communications of the EASST"} - the European Association for the Study of Science and Technology.
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\end{frame}
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