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Remove unnecessary files in results directory

Merged Dominik Burri requested to merge results_dir into dev
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@@ -159,7 +159,7 @@ rule fastqc:
shell:
"(mkdir -p {output.outdir}; \
fastqc --outdir {output.outdir} {input.reads}) \
fastqc --outdir {output.outdir} --threads {threads} {input.reads}) \
1> {log.stdout} 2> {log.stderr}"
@@ -169,16 +169,16 @@ rule create_index_star:
"""
input:
genome = lambda wildcards:
get_sample(
os.path.abspath(get_sample(
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'genome',
search_id='organism',
search_value=wildcards.organism),
search_value=wildcards.organism)),
gtf = lambda wildcards:
get_sample(
os.path.abspath(get_sample(
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'gtf',
search_id='organism',
search_value=wildcards.organism)
search_value=wildcards.organism))
output:
chromosome_info = os.path.join(
@@ -250,11 +250,11 @@ rule extract_transcriptome:
search_id='organism',
search_value=wildcards.organism)
output:
transcriptome = os.path.join(
transcriptome = temp(os.path.join(
config['output_dir'],
"transcriptome",
"{organism}",
"transcriptome.fa")
"transcriptome.fa"))
log:
stderr = os.path.join(
@@ -292,11 +292,11 @@ rule concatenate_transcriptome_and_genome:
search_value=wildcards.organism)
output:
genome_transcriptome = os.path.join(
genome_transcriptome = temp(os.path.join(
config['output_dir'],
"transcriptome",
"{organism}",
"genome_transcriptome.fa")
"genome_transcriptome.fa"))
singularity:
"docker://bash:5.0.16"
@@ -413,9 +413,9 @@ rule extract_transcripts_as_bed12:
get_sample('gtf')
output:
bed12 = os.path.join(
bed12 = temp(os.path.join(
config['output_dir'],
"full_transcripts_protein_coding.bed")
"full_transcripts_protein_coding.bed"))
singularity:
"docker://zavolab/zgtf:0.1"
@@ -515,12 +515,12 @@ rule calculate_TIN_scores:
"full_transcripts_protein_coding.bed")
output:
TIN_score = os.path.join(
TIN_score = temp(os.path.join(
config['output_dir'],
"samples",
"{sample}",
"TIN",
"TIN_score.tsv")
"TIN_score.tsv"))
params:
sample = "{sample}"
@@ -937,30 +937,32 @@ rule star_rpm:
search_value=wildcards.sample))
output:
str1 = os.path.join(
str1 = temp(os.path.join(
config["output_dir"],
"samples",
"{sample}",
"STAR_coverage",
"{sample}_Signal.Unique.str1.out.bg"),
str2 = os.path.join(
"{sample}_Signal.Unique.str1.out.bg")),
str2 = temp(os.path.join(
config["output_dir"],
"samples",
"{sample}",
"STAR_coverage",
"{sample}_Signal.UniqueMultiple.str1.out.bg"),
str3 = os.path.join(
"{sample}_Signal.UniqueMultiple.str1.out.bg")),
str3 = temp(os.path.join(
config["output_dir"],
"samples",
"{sample}",
"STAR_coverage",
"{sample}_Signal.Unique.str2.out.bg"),
str4 = os.path.join(
"{sample}_Signal.Unique.str2.out.bg")),
str4 = temp(os.path.join(
config["output_dir"],
"samples",
"{sample}",
"STAR_coverage",
"{sample}_Signal.UniqueMultiple.str2.out.bg")
"{sample}_Signal.UniqueMultiple.str2.out.bg"))
shadow: "full"
params:
out_dir = lambda wildcards, output:
@@ -1034,20 +1036,20 @@ rule rename_star_rpm_for_alfa:
search_value=wildcards.sample))
output:
plus = os.path.join(
plus = temp(os.path.join(
config["output_dir"],
"samples",
"{sample}",
"ALFA",
"{unique}",
"{sample}.{unique}.plus.bg"),
minus = os.path.join(
"{sample}.{unique}.plus.bg")),
minus = temp(os.path.join(
config["output_dir"],
"samples",
"{sample}",
"ALFA",
"{unique}",
"{sample}.{unique}.minus.bg")
"{sample}.{unique}.minus.bg"))
params:
orientation = lambda wildcards:
@@ -1081,10 +1083,10 @@ rule generate_alfa_index:
''' Generate ALFA index files from sorted GTF file '''
input:
gtf = lambda wildcards:
get_sample(
os.path.abspath(get_sample(
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'gtf',
search_id='organism',
search_value=wildcards.organism),
search_value=wildcards.organism)),
chr_len = os.path.join(
config["star_indexes"],
@@ -1164,20 +1166,20 @@ rule alfa_qc:
"sorted_genes.stranded.ALFA_index")
output:
biotypes = os.path.join(
biotypes = temp(os.path.join(
config["output_dir"],
"samples",
"{sample}",
"ALFA",
"{unique}",
"ALFA_plots.Biotypes.pdf"),
categories = os.path.join(
"ALFA_plots.Biotypes.pdf")),
categories = temp(os.path.join(
config["output_dir"],
"samples",
"{sample}",
"ALFA",
"{unique}",
"ALFA_plots.Categories.pdf"),
"ALFA_plots.Categories.pdf")),
table = os.path.join(
config["output_dir"],
"samples",
@@ -1382,13 +1384,13 @@ rule sort_bed_4_big:
"{sample}.{unique}.{strand}.bg")
output:
sorted_bg = os.path.join(
sorted_bg = temp(os.path.join(
config["output_dir"],
"samples",
"{sample}",
"bigWig",
"{unique}",
"{sample}_{unique}_{strand}.sorted.bg")
"{sample}_{unique}_{strand}.sorted.bg"))
singularity:
"docker://cjh4zavolab/bedtools:2.27"
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