diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index a68aa98..b1e5e6e 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -192,7 +192,7 @@ def get_markdup_bam(wildcards): def get_markdup_fastqc(wildcards): return expand( - fastqc_markdup_folder.joinpath("{{serie}}", "{sample}.markdup_fastqc.html"), + fastqc_markdup_folder.joinpath("{{serie}}", "{sample}.markdup_fastqc.zip"), sample=get_samples(wildcards, samples), ) @@ -262,7 +262,7 @@ def get_star_stats(wildcards): def get_star_fastqc(wildcards): return expand( fastqc_star_folder.joinpath( - "{{serie}}", "{sample}.Aligned.sortedByCoord.out_fastqc.html" + "{{serie}}", "{sample}.Aligned.sortedByCoord.out_fastqc.zip" ), sample=get_samples(wildcards, samples), ) @@ -301,17 +301,17 @@ def get_trimmed_fastqc(wildcards): if s in library_names_paired: ret = [ *expand( - fastqc_trim_folder.joinpath(wildcards.serie, "{sample}_1_fastqc.html"), + fastqc_trim_folder.joinpath(wildcards.serie, "{sample}_1_fastqc.zip"), sample=get_samples(wildcards, samples), ), *expand( - fastqc_trim_folder.joinpath(wildcards.serie, "{sample}_2_fastqc.html"), + fastqc_trim_folder.joinpath(wildcards.serie, "{sample}_2_fastqc.zip"), sample=get_samples(wildcards, samples), ), ] else: ret = expand( - fastqc_trim_folder.joinpath(wildcards.serie, "{sample}_fastqc.html"), + fastqc_trim_folder.joinpath(wildcards.serie, "{sample}_fastqc.zip"), sample=get_samples(wildcards, samples), ) return ret @@ -321,7 +321,7 @@ def get_fastqc(wildcards): s = get_samples(wildcards, samples) if wildcards.serie in library_names_single: ret = expand( - fastqc_raw_folder.joinpath(wildcards.serie, "{sample}_fastqc.html"), + fastqc_raw_folder.joinpath(wildcards.serie, "{sample}_fastqc.zip"), sample=s, ) else: @@ -351,7 +351,7 @@ def get_fastqc(wildcards): ret.append( fastqc_raw_folder.joinpath( wildcards.serie, - "{0}{1}_fastqc.html".format(sample, m[i]), + "{0}{1}_fastqc.zip".format(sample, m[i]), ) ) if not ret: