From afac6484dc8a290eb488ba216e5cf8d0de5cc28b Mon Sep 17 00:00:00 2001 From: seehagec01 <seehagec01@fu-berlin.de> Date: Mon, 21 Mar 2022 17:01:45 +0100 Subject: [PATCH] fix#2 --- tutorial/workflow/envs/yourenv.yaml | 1 + tutorial/workflow/rules/fastqc.smk | 55 ++++++++++++++++++++++++++--- 2 files changed, 52 insertions(+), 4 deletions(-) diff --git a/tutorial/workflow/envs/yourenv.yaml b/tutorial/workflow/envs/yourenv.yaml index bba82dd..0782b60 100644 --- a/tutorial/workflow/envs/yourenv.yaml +++ b/tutorial/workflow/envs/yourenv.yaml @@ -9,6 +9,7 @@ dependencies: - ca-certificates=2022.2.1=hecd8cb5_0 - certifi=2021.10.8=py37hecd8cb5_2 - curl=7.80.0=hca72f7f_0 + - fastqc=0.11.9 - krb5=1.19.2=hcd88c3b_0 - libcurl=7.80.0=h6dfd666_0 - libcxx=12.0.0=h2f01273_0 diff --git a/tutorial/workflow/rules/fastqc.smk b/tutorial/workflow/rules/fastqc.smk index 73f9dae..d647f0b 100644 --- a/tutorial/workflow/rules/fastqc.smk +++ b/tutorial/workflow/rules/fastqc.smk @@ -1,9 +1,25 @@ +#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: input: rf1 = lambda wildcards: samples.at[wildcards.sample,'fq1'] if wildcards.sample in samples.index else ' ' output: - html="results/fastqc/{sample}_1_fastqc.html", - zip="results/fastqc/{sample}_1_fastqc.zip" + html="results/fastqc/raw/{sample}_1_fastqc.html", + zip="results/fastqc/raw/{sample}_1_fastqc.zip" conda: "../envs/yourenv.yaml" log: @@ -11,15 +27,46 @@ rule rawfastqc1: wrapper: "v1.3.1/bio/fastqc" + rule rawfastqc2: input: rf2 = lambda wildcards: samples.at[wildcards.sample,'fq2'] if wildcards.sample in samples.index else ' ' output: - html="results/fastqc/{sample}_2_fastqc.html", - zip="results/fastqc/{sample}_2_fastqc.zip" + html="results/fastqc/raw/{sample}_2_fastqc.html", + zip="results/fastqc/raw/{sample}_2_fastqc.zip" conda: "../envs/yourenv.yaml" log: "workflow/report/fastqc/{sample}.log" wrapper: "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" -- GitLab