Bug fixes

.gitignore

@@ -1,6 +1,7 @@
 results/**
 resources/**
 logs/**
+config/samples.tsv
 .snakemake
 .snakemake/**
 report.zip

config/config.yaml

@@ -14,7 +14,7 @@ resources:
 scatter_items: 100
 
 # Path of the sample file
-sample_path: "/projects/koesterlab/benchmark-methylation/data_analysis_jochen/compare_meth/config/sample.tsv"
+sample_path: "config/sample.tsv"
 
 # Name of base experiment
 ref_sample: "BC01-ref-sorted"

workflow/envs/varlociraptor.yaml

@@ -1,29 +1,54 @@
-name: varlociraptor
+# name: varlociraptor
+# channels:
+#   - conda-forge
+#   - bioconda
+#   - rmg
+#   - nodefaults
+# dependencies:
+#   - alignoth=0.7.3
+#   # - bcftools=1.16
+#   # - bwa=0.7.17
+#   - bzip2=1.0.8
+#   - ca-certificates=2022.12.7
+#   - cmake=3.25.1
+#   - curl=7.87.0
+#   - expat=2.5.0
+#   - gcc=12.2.0
+#   - gsl=2.7
+#   # - htslib=1.16
+#   - make=4.3
+#   - mason=2.0.9
+#   - perl=5.32.1
+#   - pkg-config=0.29.2
+#   - rust=1.80.0
+#   # - samtools=1.16.1
+#   - xz=5.2.6
+#   # - zlib=1.2.13
+#   - zlib-ng=2.0.6
+#   - zstd=1.5.2
+#   - libclang=16.0.6
+#   - clangdev=16.0.6
+#   - libgcc-ng
+
+
 channels:
   - conda-forge
   - bioconda
   - nodefaults
 dependencies:
-  - alignoth=0.7.3
-  - bcftools=1.16
-  - bwa=0.7.17
-  - bzip2=1.0.8
-  - ca-certificates=2022.12.7
-  - cmake=3.25.1
-  - curl=7.87.0
-  - expat=2.5.0
-  - gcc=12.2.0
-  - gsl=2.7
-  - htslib=1.16
-  - make=4.3
-  - mason=2.0.9
-  - perl=5.32.1
-  - pkg-config=0.29.2
-  - rust=1.70
-  - samtools=1.16.1
-  - xz=5.2.6
-  - zlib=1.2.13
-  - zlib-ng=2.0.6
-  - zstd=1.5.2
-  - libclang=16.0.6
-  - clangdev=16.0.6
+  - varlociraptor =8.4
+  - vega-lite-cli =5.16
+  - bcftools =1.19
+  - libclang
+  - rust
+  - pkg-config
+  - make
+  - cmake
+  - gsl
+  - libcblas
+  - openssl
+  - zlib
+  - bzip2
+  - xz
+  - clangdev
+  - blis

workflow/rules/dmr_calling.smk

@@ -12,9 +12,8 @@ rule filter_calls:
         event="PRESENT",
     shell:
         """
-        PIPELINE_PATH=$(pwd)
         cd {params.varlo_path}
-        cargo run --release -- filter-calls control-fdr --mode local-smart $PIPELINE_PATH/{input} --events {params.event} --fdr 0.01 > $PIPELINE_PATH/{output}
+        cargo run --release -- filter-calls control-fdr --mode local-smart {input} --events {params.event} --fdr 0.01 > {output}
         """
 
 

workflow/rules/methylation_calling.smk

@@ -6,7 +6,7 @@ scattergather:
 rule find_candidates:
     input:
         "resources/genome.fasta",
-        varlo_path="resources/ref/varlociraptor",
+        varlo_path="resources/tools/varlociraptor",
     output:
         "resources/candidates/candidates.bcf",
     log:
@@ -15,9 +15,8 @@ rule find_candidates:
         "../envs/varlociraptor.yaml"
     shell:
         """ 
-        PIPELINE_PATH=$(pwd)
         cd {input.varlo_path}
-        cargo run -- methylation-candidates $PIPELINE_PATH/{input} $PIPELINE_PATH/{output}
+        cargo run -- methylation-candidates {input} {output}
         """
 
 
@@ -36,7 +35,7 @@ rule split_candidates:
 
 rule compute_meth_observations:
     input:
-        varlo_path="resources/ref/varlociraptor",
+        varlo_path="resources/tools/varlociraptor",
         genome="resources/genome.fasta",
         genomeIndex="resources/genome.fasta.fai",
         alignments="resources/alignments/{sample}.bam",
@@ -52,15 +51,14 @@ rule compute_meth_observations:
         sequencer=lambda wildcards: samples[wildcards.sample][1],
     shell:
         """ 
-        PIPELINE_PATH=$(pwd)
         cd {input.varlo_path}
-        cargo run --release -- preprocess variants $PIPELINE_PATH{input.genome} --candidates $PIPELINE_PATH{input.candidates} --bam $PIPELINE_PATH{input.alignments} --read-type {params.sequencer} --max-depth 1000 > $PIPELINE_PATH{output}
+        cargo run --release -- preprocess variants {input.genome} --candidates {input.candidates} --bam {input.alignments} --read-type {params.sequencer} --max-depth 1000 > {output}
         """
 
 
 rule call_methylation:
     input:
-        varlo_path="resources/ref/varlociraptor",
+        varlo_path="resources/tools/varlociraptor",
         preprocess_obs="results/{sample}/normal_{scatteritem}.bcf",
         scenario="resources/scenario.yaml",
     output:
@@ -71,9 +69,8 @@ rule call_methylation:
         "../envs/varlociraptor.yaml"
     shell:
         """ 
-        PIPELINE_PATH
         cd {input.varlo_path}
-        cargo run --release -- call variants --omit-strand-bias generic --scenario $PIPELINE_PATH{input.scenario} --obs normal=$PIPELINE_PATH{input.preprocess_obs} > $PIPELINE_PATH{output}
+        cargo run --release -- call variants --omit-strand-bias generic --scenario {input.scenario} --obs normal={input.preprocess_obs} > {output}
         """
 
 

workflow/rules/prepare_meth_calling.smk

@@ -42,8 +42,7 @@ rule genome_index:
         "../envs/samtools.yaml"
     shell:
         """ 
-        PIPELINE_PATH=$(pwd)
-        samtools faidx $PIPELINE_PATH{input}
+        samtools faidx {input}
         """
 
 
@@ -59,6 +58,5 @@ rule aligned_downsampled_index:
     threads: 10
     shell:
         """
-        PIPELINE_PATH=$(pwd)
-        samtools index -@ {threads} $PIPELINE_PATH{input}
+        samtools index -@ {threads} {input}
         """