Commit 9cc8a073 authored by Davis McCarthy's avatar Davis McCarthy
Browse files

Tweaking snakemake workflow

parent 595d0c7a
......@@ -43,9 +43,9 @@ rule all:
rule fastqc_reports:
input:
'data/fastq/{sample}.fastq.gz'
'data/fastq/{sample_long}.fastq.gz'
output:
'reports/fastqc/{sample}_fastqc.html'
'reports/fastqc/{sample_long}_fastqc.html'
params:
output_dir="reports/fastqc/"
singularity:
......@@ -56,24 +56,24 @@ rule fastqc_reports:
rule trim_fastq:
input:
lambda wildcards: expand('data/fastq/{sample_long}.fastq.gz', sample_long=SAMPLES_DICT[wildcards.sample])
'data/fastq/{sample_long}.fastq.gz'
output:
fq='data/fastq/{sample}_trimmed.fq.gz',
txt='data/fastq/{sample}.fastq.gz_trimming_report.txt'
fq='data/fastq/{sample_long}_trimmed.fq.gz',
txt='data/fastq/{sample_long}.fastq.gz_trimming_report.txt'
log:
"logs/trim_fastq/{sample}.log"
"logs/trim_fastq/{sample_long}.log"
singularity:
"docker://dmccarthy/embo-singlecellomics-methylation_2019-05_heidelberg:0.4"
shell:
'trim_galore --gzip --non_directional --rrbs '
'trim_galore --gzip --non_directional --rrbs -o data/fastq '
'{input} '
rule fastqc_reports_trimmed:
input:
'data/fastq/{sample}_trimmed.fq.gz'
'data/fastq/{sample_long}_trimmed.fq.gz'
output:
temp('reports/fastqc/{sample}_trimmed_fastqc.html')
temp('reports/fastqc/{sample_long}_trimmed_fastqc.html')
params:
output_dir="reports/fastqc/"
singularity:
......@@ -95,15 +95,15 @@ rule bismark_prepare_genome:
rule bismark:
input:
'data/fastq/{sample}_trimmed.fq.gz',
'genome/Bisulfite_Genome'
fq=lambda wildcards: expand('data/fastq/{sample_long}_trimmed.fq.gz', sample_long=SAMPLES_DICT[wildcards.sample])
gn='genome/Bisulfite_Genome'
output:
temp('data/bismark/raw/{sample}_trimmed_bismark_bt2.bam') ## CHECK BISMARK OUTPUT
singularity:
"docker://dmccarthy/embo-singlecellomics-methylation_2019-05_heidelberg:0.4"
shell:
'bismark --non_directional --genome genome -o data/bismark/raw '
'{input}'
'{input.fq}'
rule bismark_dedup:
......
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