From 510f2276a07a5941a04e719f756d7725f4c36a34 Mon Sep 17 00:00:00 2001 From: Catherine Chahrour <74187550+CChahrour@users.noreply.github.com> Date: Thu, 4 May 2023 07:54:28 +0100 Subject: [PATCH] Feat split fastq files (#65) * feat: add fastq_split option * add fastq_split option to atac chip and rna & test * add num of parts to split fastq to config * update test for snp with split and call snps --- .gitignore | 1 + environment.yml | 2 + seqnado/utils.py | 9 ++- .../config_atac/cookiecutter.json | 1 + .../config_atac.yml | 1 + .../config_chip/cookiecutter.json | 1 + .../config_chip.yml | 1 + .../config_rna/cookiecutter.json | 1 + .../config_rna.yml | 1 + .../config_snp/cookiecutter.json | 2 + .../config_snp.yml | 2 + seqnado/workflow/envs/environment.yml | 1 + .../profile_drmaa_singularity/config.yaml | 2 +- seqnado/workflow/rules/align.smk | 80 +++++++++---------- seqnado/workflow/rules/align_rna.smk | 2 +- seqnado/workflow/rules/fastq_split.smk | 69 ++++++++++++++++ seqnado/workflow/rules/qc.smk | 65 +++++++++------ seqnado/workflow/snakefile_snp | 11 ++- tests/test_atac.py | 1 + tests/test_chip.py | 11 ++- tests/test_rna.py | 12 ++- tests/test_snp.py | 2 + 22 files changed, 206 insertions(+), 72 deletions(-) create mode 100644 seqnado/workflow/rules/fastq_split.smk diff --git a/.gitignore b/.gitignore index 916d41c3..297007d9 100644 --- a/.gitignore +++ b/.gitignore @@ -12,3 +12,4 @@ dist/* .ipynb_checkpoints/ seqnado/_version.py +2023-04-27_test_snp/* diff --git a/environment.yml b/environment.yml index 8e6f4df2..f6073b38 100644 --- a/environment.yml +++ b/environment.yml @@ -4,12 +4,14 @@ channels: - bioconda - defaults dependencies: +- bedtools - bcftools - bowtie2 - click - cookiecutter - deeptools - fastqc +- fastqsplitter - homer - macs2 - multiqc diff --git a/seqnado/utils.py b/seqnado/utils.py index e3f1c8bf..f7e53f28 100644 --- a/seqnado/utils.py +++ b/seqnado/utils.py @@ -183,13 +183,20 @@ def check_options(value: object): def translate_fq_files(wc, samples: GenericFastqSamples, paired: bool=False): - if paired: return {"fq1": samples.translation[f"{wc.sample}_1.fastq.gz"], "fq2": samples.translation[f"{wc.sample}_2.fastq.gz"]} else: return {"fq": samples.translation[f"{wc.sample}_{wc.read}.fastq.gz"]} + +def translate_fq_files_split(wc, samples: GenericFastqSamples, paired: bool=False): + if paired: + return [[f"fq1=", samples.translation[f"{wc.sample}_1.fastq.gz"]], + [f"fq2=", samples.translation[f"{wc.sample}_2.fastq.gz"]]] + else: + return [f"fq=", samples.translation[f"{wc.sample}_{wc.read}.fastq.gz"]] + def get_fq_filestem(wc, samples: GenericFastqSamples): fn = samples.translation[f"{wc.sample}_{wc.read}.fastq.gz"] basename = os.path.basename(fn) diff --git a/seqnado/workflow/config/cookiecutter_config/config_atac/cookiecutter.json b/seqnado/workflow/config/cookiecutter_config/config_atac/cookiecutter.json index 05605192..09772a47 100644 --- a/seqnado/workflow/config/cookiecutter_config/config_atac/cookiecutter.json +++ b/seqnado/workflow/config/cookiecutter_config/config_atac/cookiecutter.json @@ -8,6 +8,7 @@ "indicies": "/databank/igenomes/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/genome", "gtf": "path/to/gtf", "read_type": ["paired", "single"], + "split_fastq": ["yes", "no"], "remove_pcr_duplicates_method": ["picard", "deeptools"], "shift_atac_reads": ["no", "yes"], "remove_blacklist": ["yes", "no"], diff --git a/seqnado/workflow/config/cookiecutter_config/config_atac/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_atac.yml b/seqnado/workflow/config/cookiecutter_config/config_atac/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_atac.yml index 012494bc..419e1e3a 100644 --- a/seqnado/workflow/config/cookiecutter_config/config_atac/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_atac.yml +++ b/seqnado/workflow/config/cookiecutter_config/config_atac/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_atac.yml @@ -13,6 +13,7 @@ genome: design: "design.csv" read_type: "{{cookiecutter.read_type}}" +split_fastq: "{{cookiecutter.split_fastq}}" remove_pcr_duplicates_method: "{{cookiecutter.remove_pcr_duplicates_method}}" shift_atac_reads: "{{cookiecutter.shift_atac_reads}}" diff --git a/seqnado/workflow/config/cookiecutter_config/config_chip/cookiecutter.json b/seqnado/workflow/config/cookiecutter_config/config_chip/cookiecutter.json index 41de8683..224c34b1 100644 --- a/seqnado/workflow/config/cookiecutter_config/config_chip/cookiecutter.json +++ b/seqnado/workflow/config/cookiecutter_config/config_chip/cookiecutter.json @@ -8,6 +8,7 @@ "indicies": "/databank/igenomes/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/genome", "gtf": "path/to/gtf", "read_type": ["paired", "single"], + "split_fastq": ["yes", "no"], "remove_pcr_duplicates_method": ["picard", "deeptools"], "remove_blacklist": ["yes", "no"], "blacklist": "path/to/hg38-blacklist.v2.bed.gz", diff --git a/seqnado/workflow/config/cookiecutter_config/config_chip/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_chip.yml b/seqnado/workflow/config/cookiecutter_config/config_chip/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_chip.yml index 3a16d3be..06f19851 100644 --- a/seqnado/workflow/config/cookiecutter_config/config_chip/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_chip.yml +++ b/seqnado/workflow/config/cookiecutter_config/config_chip/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_chip.yml @@ -13,6 +13,7 @@ genome: design: "design.csv" read_type: "{{cookiecutter.read_type}}" +split_fastq: "{{cookiecutter.split_fastq}}" remove_pcr_duplicates_method: "{{cookiecutter.remove_pcr_duplicates_method}}" shift_atac_reads: "False" diff --git a/seqnado/workflow/config/cookiecutter_config/config_rna/cookiecutter.json b/seqnado/workflow/config/cookiecutter_config/config_rna/cookiecutter.json index 40c6bc10..2870264e 100644 --- a/seqnado/workflow/config/cookiecutter_config/config_rna/cookiecutter.json +++ b/seqnado/workflow/config/cookiecutter_config/config_rna/cookiecutter.json @@ -8,6 +8,7 @@ "indicies": "/databank/igenomes/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/genome", "gtf": "/databank/igenomes/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf", "read_type": ["paired", "single"], + "split_fastq": ["yes", "no"], "remove_pcr_duplicates_method": ["picard", "deeptools"], "remove_blacklist": ["yes", "no"], "blacklist": "path/to/hg38-blacklist.v2.bed.gz", diff --git a/seqnado/workflow/config/cookiecutter_config/config_rna/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_rna.yml b/seqnado/workflow/config/cookiecutter_config/config_rna/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_rna.yml index 5fc79bb7..a236bf21 100644 --- a/seqnado/workflow/config/cookiecutter_config/config_rna/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_rna.yml +++ b/seqnado/workflow/config/cookiecutter_config/config_rna/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_rna.yml @@ -17,6 +17,7 @@ genome: design: "design.csv" read_type: "{{cookiecutter.read_type}}" +split_fastq: "{{cookiecutter.split_fastq}}" remove_pcr_duplicates_method: "{{cookiecutter.remove_pcr_duplicates_method}}" shift_atac_reads: "False" diff --git a/seqnado/workflow/config/cookiecutter_config/config_snp/cookiecutter.json b/seqnado/workflow/config/cookiecutter_config/config_snp/cookiecutter.json index 23b314aa..24dadbaa 100644 --- a/seqnado/workflow/config/cookiecutter_config/config_snp/cookiecutter.json +++ b/seqnado/workflow/config/cookiecutter_config/config_snp/cookiecutter.json @@ -9,6 +9,8 @@ "chromosome_sizes": "path/to/hg38.chrom.sizes", "indicies": "/databank/igenomes/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/genome", "read_type": ["paired", "single"], + "split_fastq": ["yes", "no"], + "split_fastq_parts": "int", "remove_blacklist": ["yes", "no"], "blacklist": "path/to/hg38-blacklist.v2.bed.gz", "call_snps": ["yes", "no"], diff --git a/seqnado/workflow/config/cookiecutter_config/config_snp/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_snp.yml b/seqnado/workflow/config/cookiecutter_config/config_snp/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_snp.yml index ade2a1b3..61e6cafc 100644 --- a/seqnado/workflow/config/cookiecutter_config/config_snp/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_snp.yml +++ b/seqnado/workflow/config/cookiecutter_config/config_snp/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_snp.yml @@ -12,6 +12,8 @@ genome: chromosome_sizes: "{{cookiecutter.chromosome_sizes}}" read_type: "{{cookiecutter.read_type}}" +split_fastq: "{{cookiecutter.split_fastq}}" +split_fastq_parts: "{{cookiecutter.split_fastq_parts}}" shift_atac_reads: "no" remove_blacklist: "{{cookiecutter.remove_blacklist}}" call_snps: "{{cookiecutter.call_snps}}" diff --git a/seqnado/workflow/envs/environment.yml b/seqnado/workflow/envs/environment.yml index cd683979..e36da0aa 100644 --- a/seqnado/workflow/envs/environment.yml +++ b/seqnado/workflow/envs/environment.yml @@ -15,6 +15,7 @@ dependencies: - deeptools - trim-galore - fastqc + - fastqsplitter - multiqc - trackhub - seaborn diff --git a/seqnado/workflow/envs/profiles/profile_drmaa_singularity/config.yaml b/seqnado/workflow/envs/profiles/profile_drmaa_singularity/config.yaml index 88d31cda..ecb377e8 100644 --- a/seqnado/workflow/envs/profiles/profile_drmaa_singularity/config.yaml +++ b/seqnado/workflow/envs/profiles/profile_drmaa_singularity/config.yaml @@ -1,5 +1,5 @@ jobname: smk-{jobid}-{rule}-{wildcards} -drmaa: --cpus-per-task={threads} --mem-per-cpu={resources.mem_mb} --time=1:00:00 +drmaa: --cpus-per-task={threads} --mem-per-cpu={resources.mem_mb} --time=24:00:00 use-singularity: true singularity-args: -B /ceph -B /databank -B /datashare jobs: 50 diff --git a/seqnado/workflow/rules/align.smk b/seqnado/workflow/rules/align.smk index 2c96d030..8c22d5ca 100644 --- a/seqnado/workflow/rules/align.smk +++ b/seqnado/workflow/rules/align.smk @@ -1,44 +1,44 @@ import seqnado.utils as utils +if config["split_fastq"] == "no": + rule align_paired: + input: + fq1="seqnado_output/trimmed/{sample}_1.fastq.gz", + fq2="seqnado_output/trimmed/{sample}_2.fastq.gz", + params: + index=config["genome"]["indicies"], + options=utils.check_options(config["bowtie2"]["options"]), + output: + bam="seqnado_output/aligned/raw/{sample}.bam", + threads: config["bowtie2"]["threads"] + resources: + mem_mb=4000 // int(config["bowtie2"]["threads"]) + log: + "seqnado_output/logs/align/{sample}.log", + shell: + """bowtie2 -p {threads} -x {params.index} -1 {input.fq1} -2 {input.fq2} {params.options} 2> {log} | + samtools view -bS - > {output.bam} && + samtools sort -@ {threads} -o {output.bam}_sorted {output.bam} >> {log} 2>&1 && + mv {output.bam}_sorted {output.bam} + """ -rule align_paired: - input: - fq1="seqnado_output/trimmed/{sample}_1.fastq.gz", - fq2="seqnado_output/trimmed/{sample}_2.fastq.gz", - params: - index=config["genome"]["indicies"], - options=utils.check_options(config["bowtie2"]["options"]), - output: - bam=temp("seqnado_output/aligned/raw/{sample}.bam"), - threads: config["bowtie2"]["threads"] - resources: - mem_mb=4000 // int(config["bowtie2"]["threads"]) - log: - "seqnado_output/logs/align/{sample}.log", - shell: - """bowtie2 -p {threads} -x {params.index} -1 {input.fq1} -2 {input.fq2} {params.options} 2> {log} | - samtools view -bS - > {output.bam} && - samtools sort -@ {threads} -o {output.bam}_sorted {output.bam} >> {log} 2>&1 && - mv {output.bam}_sorted {output.bam} - """ - -# rule align_single: -# input: -# fq1="seqnado_output/trimmed/{sample}.fastq.gz", -# params: -# index=config["genome"]["indicies"], -# options=config["bowtie2"]["options"], -# output: -# bam=temp("seqnado_output/aligned/raw/{sample}.bam"), -# resources: -# mem_mb=4000 // int(config["bowtie2"]["threads"]) -# threads: config["bowtie2"]["threads"] -# log: -# "seqnado_output/logs/align/{sample}.log", -# shell: -# """bowtie2 -p {threads} -x {params.index} -U {input.fq1} {params.options} 2> {log} | -# samtools view -bS - > {output.bam} && -# samtools sort -@ {threads} -o {output.bam}_sorted {output.bam} && -# mv {output.bam}_sorted {output.bam} -# """ + # rule align_single: + # input: + # fq1="seqnado_output/trimmed/{sample}.fastq.gz", + # params: + # index=config["genome"]["indicies"], + # options=config["bowtie2"]["options"], + # output: + # bam=temp("seqnado_output/aligned/raw/{sample}.bam"), + # resources: + # mem_mb=4000 // int(config["bowtie2"]["threads"]) + # threads: config["bowtie2"]["threads"] + # log: + # "seqnado_output/logs/align/{sample}.log", + # shell: + # """bowtie2 -p {threads} -x {params.index} -U {input.fq1} {params.options} 2> {log} | + # samtools view -bS - > {output.bam} && + # samtools sort -@ {threads} -o {output.bam}_sorted {output.bam} && + # mv {output.bam}_sorted {output.bam} + # """ diff --git a/seqnado/workflow/rules/align_rna.smk b/seqnado/workflow/rules/align_rna.smk index 91b36680..245d81cd 100644 --- a/seqnado/workflow/rules/align_rna.smk +++ b/seqnado/workflow/rules/align_rna.smk @@ -31,7 +31,7 @@ rule rename_aligned: input: bam=rules.align_paired.output.bam, output: - bam="seqnado_output/aligned/sorted/{sample}.bam", + bam="seqnado_output/aligned/raw/{sample}.bam", shell: "mv {input.bam} {output.bam}" diff --git a/seqnado/workflow/rules/fastq_split.smk b/seqnado/workflow/rules/fastq_split.smk new file mode 100644 index 00000000..990f530d --- /dev/null +++ b/seqnado/workflow/rules/fastq_split.smk @@ -0,0 +1,69 @@ +import seqnado.utils as utils +PARTS=[str (x) for x in range(int(config["split_fastq_parts"]))] +if config["split_fastq"] == "yes": + if config["read_type"] == "paired": + rule split_fq: + input: + unpack(lambda wc: seqnado.utils.translate_fq_files(wc, samples=FASTQ_SAMPLES, paired=True)), + output: + expand("seqnado_output/fastq_split/{{sample}}_{part}_{read}.fastq.gz", part=PARTS, read=["1", "2"]), + params: + split1=expand("-o seqnado_output/fastq_split/{{sample}}_{part}_1.fastq.gz", part=PARTS), + split2=expand("-o seqnado_output/fastq_split/{{sample}}_{part}_2.fastq.gz", part=PARTS), + resources: + mem_mb=750, + shell:""" + fastqsplitter -i {input.fq1} {params.split1} && + fastqsplitter -i {input.fq2} {params.split2} + """ + + rule trimgalore_paired: + input: + split1="seqnado_output/fastq_split/{sample}_{part}_1.fastq.gz", + split2="seqnado_output/fastq_split/{sample}_{part}_2.fastq.gz", + output: + trimmed1=temp("seqnado_output/trimmed/{sample}_{part}_1_trimmed.fq.gz"), + trimmed2=temp("seqnado_output/trimmed/{sample}_{part}_2_trimmed.fq.gz"), + threads: 4 + resources: + mem_mb=750, + params: + options=utils.check_options(config['trim_galore']['options']), + trim_dir="seqnado_output/trimmed" + log:"seqnado_output/logs/trimming/{sample}_{part}.log", + shell:""" + trim_galore --cores {threads} {params.options} --basename {wildcards.sample}_{wildcards.part} --paired --output_dir {params.trim_dir} {input.split1} {input.split2} >> {log} 2>&1 && + mv {params.trim_dir}/{wildcards.sample}_{wildcards.part}_val_1.fq.gz {output.trimmed1} && + mv {params.trim_dir}/{wildcards.sample}_{wildcards.part}_val_2.fq.gz {output.trimmed2} + """ + + rule align_split: + input: + fq1="seqnado_output/trimmed/{sample}_{part}_1_trimmed.fq.gz", + fq2="seqnado_output/trimmed/{sample}_{part}_2_trimmed.fq.gz", + output: + bam=temp("seqnado_output/aligned/split/{sample}_{part}.bam"), + params: + index=config["genome"]["indicies"], + options=utils.check_options(config["bowtie2"]["options"]), + threads: config["bowtie2"]["threads"] + resources: + mem_mb=4000 // int(config["bowtie2"]["threads"]) + log:"seqnado_output/logs/aligned/split/{sample}_part{part}.log", + shell:""" + bowtie2 -p {threads} -x {params.index} -1 {input.fq1} -2 {input.fq2} {params.options} 2> {log} | + samtools view -bS - > {output.bam} && + samtools sort -@ {threads} -o {output.bam}_sorted {output.bam} >> {log} 2>&1 && + mv {output.bam}_sorted {output.bam} + """ + + rule merge_bams: + input: + expand("seqnado_output/aligned/split/{{sample}}_{part}.bam", part=PARTS), + output: + bam=temp("seqnado_output/aligned/raw/{sample}.bam"), + threads: 4 + log:"seqnado_output/logs/merge/{sample}.log", + shell:""" + samtools merge -o {output.bam} -@ {threads} -h {input} >> {log} 2>&1 + """ diff --git a/seqnado/workflow/rules/qc.smk b/seqnado/workflow/rules/qc.smk index e5c08548..b2bd2972 100644 --- a/seqnado/workflow/rules/qc.smk +++ b/seqnado/workflow/rules/qc.smk @@ -42,7 +42,7 @@ rule fastqc_trimmed: rule samtools_stats: input: - bam="seqnado_output/aligned/sorted/{sample}.bam", + bam="seqnado_output/aligned/raw/{sample}.bam", output: stats="seqnado_output/qc/alignment_raw/{sample}.txt", threads: 1 @@ -58,26 +58,45 @@ use rule samtools_stats as samtools_stats_filtered with: output: stats="seqnado_output/qc/alignment_filtered/{sample}.txt", +if config["split_fastq"] == "no": + rule multiqc: + input: + expand( + "seqnado_output/qc/fastqc_raw/{sample}_{read}_fastqc.html", + sample=SAMPLE_NAMES, + read=[1, 2], + ), + expand( + "seqnado_output/qc/fastqc_trimmed/{sample}_{read}_fastqc.html", + sample=SAMPLE_NAMES, + read=[1, 2], + ), + expand("seqnado_output/qc/alignment_raw/{sample}.txt", sample=SAMPLE_NAMES), + expand("seqnado_output/qc/alignment_filtered/{sample}.txt", sample=SAMPLE_NAMES), + output: + "seqnado_output/qc/full_qc_report.html", + log: + "seqnado_output/logs/multiqc.log", + resources: + mem_mb=1000, + shell: + "multiqc -o seqnado_output/qc seqnado_output/qc -n full_qc_report.html --force > {log} 2>&1" -rule multiqc: - input: - expand( - "seqnado_output/qc/fastqc_raw/{sample}_{read}_fastqc.html", - sample=SAMPLE_NAMES, - read=[1, 2], - ), - expand( - "seqnado_output/qc/fastqc_trimmed/{sample}_{read}_fastqc.html", - sample=SAMPLE_NAMES, - read=[1, 2], - ), - expand("seqnado_output/qc/alignment_raw/{sample}.txt", sample=SAMPLE_NAMES), - expand("seqnado_output/qc/alignment_filtered/{sample}.txt", sample=SAMPLE_NAMES), - output: - "seqnado_output/qc/full_qc_report.html", - log: - "seqnado_output/logs/multiqc.log", - resources: - mem_mb=1000, - shell: - "multiqc -o seqnado_output/qc seqnado_output/qc -n full_qc_report.html --force > {log} 2>&1" +else: + rule multiqc: + input: + expand( + "seqnado_output/qc/fastqc_raw/{sample}_{read}_fastqc.html", + sample=SAMPLE_NAMES, + read=[1, 2], + ), + expand("seqnado_output/qc/alignment_raw/{sample}.txt", sample=SAMPLE_NAMES), + expand("seqnado_output/qc/alignment_filtered/{sample}.txt", sample=SAMPLE_NAMES), + output: + "seqnado_output/qc/full_qc_report.html", + log: + "seqnado_output/logs/multiqc.log", + resources: + mem_mb=1000, + shell: + "multiqc -o seqnado_output/qc seqnado_output/qc -n full_qc_report.html --force > {log} 2>&1" diff --git a/seqnado/workflow/snakefile_snp b/seqnado/workflow/snakefile_snp index 9640eda1..8e5506b4 100755 --- a/seqnado/workflow/snakefile_snp +++ b/seqnado/workflow/snakefile_snp @@ -35,12 +35,15 @@ else: DESIGN = FASTQ_SAMPLES.design SAMPLE_NAMES = FASTQ_SAMPLES.sample_names_all - -include: "rules/qc.smk" -include: "rules/fastq_trim.smk" -include: "rules/align.smk" include: "rules/alignment_post_processing.smk" +include: "rules/qc.smk" include: "rules/variant.smk" +if config["split_fastq"] == "yes": + include: "rules/fastq_split.smk" +else: + include: "rules/fastq_trim.smk" + include: "rules/align.smk" + # Define output files ANALYSIS_OUTPUT = [ diff --git a/tests/test_atac.py b/tests/test_atac.py index 6f4c972f..c9d2000d 100644 --- a/tests/test_atac.py +++ b/tests/test_atac.py @@ -121,6 +121,7 @@ def set_up( "indicies": genome_indicies, "design": "design.csv", "read_type": "paired", + "split_fastq": "no", "remove_pcr_duplicates_method": "picard", "shift_atac_reads": "yes", "remove_blacklist": "yes", diff --git a/tests/test_chip.py b/tests/test_chip.py index 80ac3882..7418ddea 100644 --- a/tests/test_chip.py +++ b/tests/test_chip.py @@ -119,9 +119,18 @@ def set_up( "project_name": "test", "chromosome_sizes": chromsizes, "indicies": genome_indicies, + "design": "design.csv", + "read_type": "paired", + "split_fastq": "no", + "remove_pcr_duplicates_method": "picard", + "shift_atac_reads": "no", + "remove_blacklist": "yes", + "blacklist": f"{data_path}/genome/hg19-blacklist.v2.chr21.bed.gz", + "make_bigwigs": "yes", "pileup_method": "deeptools", + "make_heatmaps": "yes", + "call_peaks": "yes", "peak_calling_method": "lanceotron", - "remove_pcr_duplicates_method": "picard", "make_ucsc_hub": "no", "UCSC_hub_directory": "test_hub", "email": "test", diff --git a/tests/test_rna.py b/tests/test_rna.py index daac46c7..fd7cb595 100644 --- a/tests/test_rna.py +++ b/tests/test_rna.py @@ -128,8 +128,18 @@ def set_up( "project_name": "test", "chromosome_sizes": chromsizes, "indicies": genome_indicies, + "design": "design.csv", + "read_type": "paired", + "split_fastq": "no", + "remove_pcr_duplicates_method": "picard", + "shift_atac_reads": "no", "remove_blacklist": "yes", - "blacklist": f"{data_path}/genome/hg19_blacklist.bed", + "blacklist": f"{data_path}/genome/hg19-blacklist.v2.chr21.bed.gz", + "make_bigwigs": "yes", + "pileup_method": "deeptools", + "make_heatmaps": "yes", + "call_peaks": "yes", + "peak_calling_method": "lanceotron", "make_ucsc_hub": "no", "UCSC_hub_directory": "test_hub", "email": "test", diff --git a/tests/test_snp.py b/tests/test_snp.py index b0ca8fdc..6d0ca48c 100644 --- a/tests/test_snp.py +++ b/tests/test_snp.py @@ -121,6 +121,8 @@ def set_up( "indicies": genome_indicies, "design": "design.csv", "read_type": "paired", + "split_fastq": "yes", + "split_fastq_parts": "10", "remove_pcr_duplicates_method": "picard", "remove_blacklist": "yes", "blacklist": f"{data_path}/genome/hg19-blacklist.v2.chr21.bed.gz",