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Commit a54ff3e8 authored by Dominik Burri's avatar Dominik Burri Committed by BIOPZ-Gypas Foivos
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Generate bedgraph file of normalised coverage. Fixes #45

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Snakefile
+ 12
− 1
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......@@ -99,7 +99,18 @@ rule finish:
"summary_salmon",
"quantmerge",
"transcripts_{salmon_merge_on}.tsv"),
salmon_merge_on=["tpm", "numreads"])
salmon_merge_on=["tpm", "numreads"]),
star_rpm = expand(
os.path.join(
config["output_dir"],
"{seqmode}",
"{sample}",
"STAR_coverage",
"{sample}_Signal.UniqueMultiple.str1.out.bg"),
zip,
sample=[i for i in list(samples_table.index.values)],
seqmode=[samples_table.loc[i, 'seqmode']
for i in list(samples_table.index.values)])
......
images/dag_test_workflow.svg
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− 227
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images/rule_graph.svg
+ 244
− 196
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tests/test_integration_workflow/expected_output.md5
+ 8
− 0
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......@@ -78,4 +78,12 @@ e72f5d798c99272f8c0166dc77247db1 results/single_end/synthetic_10_reads_mate_1_s
92bcd0592d22a6a58d0360fc76103e56 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/observed_bias
92bcd0592d22a6a58d0360fc76103e56 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/observed_bias_3p
d41d8cd98f00b204e9800998ecf8427e results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/unmapped_names.txt
0139e75ddbfe6eb081c2c2d9b9108ab4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.str1.out.bg
c266d31e0a2ad84975cb9de335891e64 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.str2.out.bg
0139e75ddbfe6eb081c2c2d9b9108ab4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.Unique.str1.out.bg
c266d31e0a2ad84975cb9de335891e64 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.Unique.str2.out.bg
ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.str1.out.bg
ede14ac41c10067838f375106fce4852 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.str2.out.bg
ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str1.out.bg
ede14ac41c10067838f375106fce4852 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str2.out.bg
79fc3e46b3ac1a72b80cb7bebf6058cd results/transcriptome/homo_sapiens/transcriptome.fa
workflow/rules/paired_end.snakefile.smk
+ 74
− 0
View file @ a54ff3e8
......@@ -453,3 +453,77 @@ rule pe_genome_quantification_kallisto:
{params.directionality} \
{input.reads1} {input.reads2} > {output.pseudoalignment}) \
2> {log.stderr}"
rule star_rpm_paired_end:
''' Create stranded bedgraph coverage with STARs RPM normalisation '''
input:
bam = os.path.join(
config["output_dir"],
"paired_end",
"{sample}",
"map_genome",
"{sample}_Aligned.sortedByCoord.out.bam"),
bai = os.path.join(
config["output_dir"],
"paired_end",
"{sample}",
"map_genome",
"{sample}_Aligned.sortedByCoord.out.bam.bai")
output:
str1 = (os.path.join(
config["output_dir"],
"paired_end",
"{sample}",
"STAR_coverage",
"{sample}_Signal.Unique.str1.out.bg"),
os.path.join(
config["output_dir"],
"paired_end",
"{sample}",
"STAR_coverage",
"{sample}_Signal.UniqueMultiple.str1.out.bg")),
str2 = (os.path.join(
config["output_dir"],
"paired_end",
"{sample}",
"STAR_coverage",
"{sample}_Signal.Unique.str2.out.bg"),
os.path.join(
config["output_dir"],
"paired_end",
"{sample}",
"STAR_coverage",
"{sample}_Signal.UniqueMultiple.str2.out.bg"))
params:
out_dir = lambda wildcards, output: os.path.dirname(output.str1[0]),
prefix = lambda wildcards, output: os.path.join(os.path.dirname(output.str1[0]),
str(wildcards.sample) + "_"),
stranded = "Stranded"
singularity:
"docker://zavolab/star:2.7.3a-slim"
log:
stderr = os.path.join(
config["log_dir"],
"paired_end",
"{sample}",
"star_rpm_paired_end.stderr.log"),
stdout = os.path.join(
config["log_dir"],
"paired_end",
"{sample}",
"star_rpm_paired_end.stdout.log")
threads: 4
shell:
"""
(mkdir -p {params.out_dir}; \
chmod -R 777 {params.out_dir}; \
STAR \
--runMode inputAlignmentsFromBAM \
--runThreadN {threads} \
--inputBAMfile {input.bam} \
--outWigType "bedGraph" \
--outWigStrand "{params.stranded}" \
--outWigNorm "RPM" \
--outFileNamePrefix {params.prefix}) \
1> {log.stdout} 2> {log.stderr}
"""
workflow/rules/single_end.snakefile.smk
+ 74
− 0
View file @ a54ff3e8
......@@ -412,3 +412,77 @@ rule genome_quantification_kallisto:
{params.directionality} \
{input.reads} > {output.pseudoalignment};) \
2> {log.stderr}"
rule star_rpm_single_end:
''' Create stranded bedgraph coverage with STARs RPM normalisation '''
input:
bam = os.path.join(
config["output_dir"],
"single_end",
"{sample}",
"map_genome",
"{sample}_Aligned.sortedByCoord.out.bam"),
bai = os.path.join(
config["output_dir"],
"single_end",
"{sample}",
"map_genome",
"{sample}_Aligned.sortedByCoord.out.bam.bai")
output:
str1 = (os.path.join(
config["output_dir"],
"single_end",
"{sample}",
"STAR_coverage",
"{sample}_Signal.Unique.str1.out.bg"),
os.path.join(
config["output_dir"],
"single_end",
"{sample}",
"STAR_coverage",
"{sample}_Signal.UniqueMultiple.str1.out.bg")),
str2 = (os.path.join(
config["output_dir"],
"single_end",
"{sample}",
"STAR_coverage",
"{sample}_Signal.Unique.str2.out.bg"),
os.path.join(
config["output_dir"],
"single_end",
"{sample}",
"STAR_coverage",
"{sample}_Signal.UniqueMultiple.str2.out.bg"))
params:
out_dir = lambda wildcards, output: os.path.dirname(output.str1[0]),
prefix = lambda wildcards, output: os.path.join(os.path.dirname(output.str1[0]),
str(wildcards.sample) + "_"),
stranded = "Stranded"
singularity:
"docker://zavolab/star:2.7.3a-slim"
log:
stderr = os.path.join(
config["log_dir"],
"single_end",
"{sample}",
"star_rpm_single_end.stderr.log"),
stdout = os.path.join(
config["log_dir"],
"single_end",
"{sample}",
"star_rpm_single_end.stdout.log")
threads: 4
shell:
"""
(mkdir -p {params.out_dir}; \
chmod -R 777 {params.out_dir}; \
STAR \
--runMode inputAlignmentsFromBAM \
--runThreadN {threads} \
--inputBAMfile {input.bam} \
--outWigType "bedGraph" \
--outWigStrand {params.stranded} \
--outWigNorm "RPM" \
--outFileNamePrefix {params.prefix}) \
1> {log.stdout} 2> {log.stderr}
"""
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