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Commit afac6484 authored by seehagec01's avatar seehagec01
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fix#2

parent 33a80bfa
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...@@ -9,6 +9,7 @@ dependencies: ...@@ -9,6 +9,7 @@ dependencies:
- ca-certificates=2022.2.1=hecd8cb5_0 - ca-certificates=2022.2.1=hecd8cb5_0
- certifi=2021.10.8=py37hecd8cb5_2 - certifi=2021.10.8=py37hecd8cb5_2
- curl=7.80.0=hca72f7f_0 - curl=7.80.0=hca72f7f_0
- fastqc=0.11.9
- krb5=1.19.2=hcd88c3b_0 - krb5=1.19.2=hcd88c3b_0
- libcurl=7.80.0=h6dfd666_0 - libcurl=7.80.0=h6dfd666_0
- libcxx=12.0.0=h2f01273_0 - libcxx=12.0.0=h2f01273_0
......
#map_dict = {'1':'fq1', '2':'fq2'}
#rule rawfastqc:
#input:
#rf1 = lambda wildcards: samples.at[wildcards.sample,map_dict[wildcards.i]] if wildcards.sample in samples.index else ' '
#rf2 = lambda wildcards: samples.at[wildcards.sample,map_dict[wildcards.i]] if wildcards.sample in samples.index else ' '
#output:
#html="results/fastqc/{sample}_{i}_fastqc.html",
#zip="results/fastqc/{sample}_{i}_fastqc.zip"
#conda:
#"../envs/yourenv.yaml"
#log:
#"workflow/report/fastqc/{sample}_{i}.log"
#wrapper:
#"v1.3.1/bio/fastqc"
rule rawfastqc1: rule rawfastqc1:
input: input:
rf1 = lambda wildcards: samples.at[wildcards.sample,'fq1'] if wildcards.sample in samples.index else ' ' rf1 = lambda wildcards: samples.at[wildcards.sample,'fq1'] if wildcards.sample in samples.index else ' '
output: output:
html="results/fastqc/{sample}_1_fastqc.html", html="results/fastqc/raw/{sample}_1_fastqc.html",
zip="results/fastqc/{sample}_1_fastqc.zip" zip="results/fastqc/raw/{sample}_1_fastqc.zip"
conda: conda:
"../envs/yourenv.yaml" "../envs/yourenv.yaml"
log: log:
...@@ -11,15 +27,46 @@ rule rawfastqc1: ...@@ -11,15 +27,46 @@ rule rawfastqc1:
wrapper: wrapper:
"v1.3.1/bio/fastqc" "v1.3.1/bio/fastqc"
rule rawfastqc2: rule rawfastqc2:
input: input:
rf2 = lambda wildcards: samples.at[wildcards.sample,'fq2'] if wildcards.sample in samples.index else ' ' rf2 = lambda wildcards: samples.at[wildcards.sample,'fq2'] if wildcards.sample in samples.index else ' '
output: output:
html="results/fastqc/{sample}_2_fastqc.html", html="results/fastqc/raw/{sample}_2_fastqc.html",
zip="results/fastqc/{sample}_2_fastqc.zip" zip="results/fastqc/raw/{sample}_2_fastqc.zip"
conda: conda:
"../envs/yourenv.yaml" "../envs/yourenv.yaml"
log: log:
"workflow/report/fastqc/{sample}.log" "workflow/report/fastqc/{sample}.log"
wrapper: wrapper:
"v1.3.1/bio/fastqc" "v1.3.1/bio/fastqc"
rule trimmedfastqc1:
input:
"results/trimmed/{sample}_forward_paired.fq.gz",
"results/trimmed/{sample}_reverse_paired.fq.gz"
output:
html="results/fastqc/trimmed/{sample}_1_fastqc.html",
zip="results/fastqc/trimmed/{sample}_1_fastqc.zip"
conda:
"../envs/yourenv.yaml"
log:
"workflow/report/fastqc/trimmed_{sample}.log"
wrapper:
"v1.3.1/bio/fastqc"
rule trimmedfastqc2:
input:
"results/trimmed/{sample}_forward_paired.fq.gz",
"results/trimmed/{sample}_reverse_paired.fq.gz"
output:
html="results/fastqc/trimmed/{sample}_2_fastqc.html",
zip="results/fastqc/trimmed/{sample}_2_fastqc.zip"
conda:
"../envs/yourenv.yaml"
log:
"workflow/report/fastqc/trimmed_{sample}.log"
wrapper:
"v1.3.1/bio/fastqc"
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