Template snakemake project for the analysis of ATAC-Seq data

public 1yr ago 0 bookmarks

View Workflow

Help improve this workflow!

This workflow has been published but could be further improved with some additional meta data:

Keyword(s) in categories input, output, operation, topic

You can help improve this workflow by suggesting the addition or removal of keywords, suggest changes and report issues, or request to become a maintainer of the Workflow .

Setting up the compute environment

Running the pipeline

Setting up the compute environment

To bui

Code Snippets

shell:
    "bwa index {input.fasta_path}"
    " && check_directory -o {output.rc}"
    " {params.index_files} {params.index_dir}"

SnakeMake BWA From line 87 of main/Snakefile

shell:
    "mkdir -p data/align/ &&"
    " bwa mem {params.extra_args} -t {params.threads}"
    " {params.ref_prefix} {input.reads1} {input.reads2}"
    " | samtools sort -@ {params.threads} -o {output.bam} -"
    " && samtools index {output.bam}"

SnakeMake SAMtools BWA From line 108 of main/Snakefile

shell:
    "mkdir -p {params.tmp_dir} {params.metrics_dir} && "
    "java -Xms{resources.java_mem_min}m -Xmx{resources.java_mem_max}m"
    " -jar $PICARD MarkDuplicates"
    " I={input.bam} M={output.metrics} TMP_DIR={params.tmp_dir}"
    " O={output.bam_dedup} REMOVE_DUPLICATES=true"
    " {params.extra_args} 2> {resources.logs}/{resources.job_id}.MD.log"
    " && samtools index {output.bam_dedup}"

SnakeMake SAMtools From line 135 of main/Snakefile

shell:
    "samtools view -@ {resources.cpus_per_node}"
    " -b {input.dedup_bam} {params.allowed_chrs}"
    " > {output.prefilt_bam} && samtools index {output.prefilt_bam} && "
    "alignmentSieve -p max -b {output.prefilt_bam} -o {output.filt_bam}"
    " --ATACshift --blackListFileName {input.blacklist}"
    " --filterMetrics {output.filt_metrics} {params.extra_args} && "
    "samtools sort -@ {resources.cpus_per_node} -o {output.filt_sort_bam}"
    " {output.filt_bam} && samtools index {output.filt_sort_bam}"

SnakeMake SAMtools DeepTools From line 165 of main/Snakefile

shell:
    "mkdir -p {params.tmp_dir} && cd {params.tmp_dir} && "
    "samtools merge -@{resources.cpus_per_node}"
    " {output.merged_bam} {input.bams} && "
    "samtools index -@{resources.cpus_per_node} {output.merged_bam}"

SnakeMake SAMtools From line 192 of main/Snakefile

shell:
    "mkdir -p {params.wig_dir} && "
    "bamCoverage --binSize {params.binsize}"
    " --normalizeUsing {params.norm_strategy}"
    " --effectiveGenomeSize {params.effective_gen_size}"
    " --numberOfProcessors {resources.cpus_per_node}"
    " -b {input.merged_bam} -o {output.bw}"

SnakeMake DeepTools From line 213 of main/Snakefile

shell:
   "mkdir -p {params.peaks_dir} && "
   "macs2 callpeak -f BAMPE --call-summits"
   " -t {input.merged_bam} --outdir {params.peaks_dir}"
   " -g hs -B -q {params.qvalue_thresh}"
   " -n {resources.job_id} {params.extra_args} && "
   "bedtools slop -i {output.summits_bed}"
   " -g {input.genome_size} -b {params.fixed_width_ext}"
   " > {output.narrow_peak_fw}"

SnakeMake BEDTools macs2 From line 238 of main/Snakefile

shell:
    "cat {input.sample_beds} | sort -k1,1V -k2,2n -k3,3n > {output.comb_sorted} && "
    "bedtools merge -i {output.comb_sorted} -c 4,5,5,5 -o collapse,min,max,mean -delim '|'"
    " > {output.merged_sorted}"