Input JSON for ``atac.wdl`` =========================== .. toctree:: :maxdepth: 2 :caption: Contents: Optional parameters and flags are marked with ``?``. #. Reference genome Currently supported genomes: * hg38: ENCODE `GRCh38_no_alt_analysis_set_GCA_000001405 `_ * mm10: ENCODE `mm10_no_alt_analysis_set_ENCODE `_ * hg19: ENCODE `GRCh37/hg19 `_ * mm9: `mm9, NCBI Build 37 `_ This TSV file has all genome specific data parameters and file path/URIs. Choose one of TSVs in ``genome`` directory. * ``"atac.genome_tsv"`` : TSV file path/URI. #. Input genome data files Choose any genome data type you want to start with and do not define others. For FASTQs and their adapters, we provide two ways to define them since DNANexus website UI only supports 1-dim array as inputs. Choose between ``fastqs`` or ``fastqs_rep[REP_ID]_R[READ_END_ID]`` for your preference. The pipeline supports up to 4 replicates. * ``"atac.fastqs"``? : 3-dimensional array with FASTQ file path/URI. - 1st dimension: replicate ID - 2nd dimension: merge ID (this dimension will be reduced after merging FASTQs) - 3rd dimension: endedness ID (0 for SE and 0,1 for PE) * ``"atac.fastqs_rep1_R1"``? : Array of FASTQ file to be merged for rep1-R1. * ``"atac.fastqs_rep1_R2"``? : Array of FASTQ file to be merged for rep1-R2. Do not define if your FASTQ is single ended. * ``"atac.fastqs_rep2_R1"``? : Array of FASTQ file to be merged for rep2-R1. Do not define if you don't have replicate 2. * ``"atac.fastqs_rep2_R2"``? : Array of FASTQ file to be merged for rep2-R2. Do not define if you don't have replicate 2. * ``"atac.fastqs_rep3_R1"``? : Array of FASTQ file to be merged for rep3-R1. Do not define if you don't have replicate 3. * ``"atac.fastqs_rep3_R2"``? : Array of FASTQ file to be merged for rep3-R2. Do not define if you don't have replicate 3. * ``"atac.fastqs_rep4_R1"``? : Array of FASTQ file to be merged for rep4-R1. Do not define if you don't have replicate 4. * ``"atac.fastqs_rep4_R2"``? : Array of FASTQ file to be merged for rep4-R2. Do not define if you don't have replicate 4. * ``"atac.bams"``? : Array of raw (unfiltered) BAM file path/URI. - 1st dimension: replicate ID * ``"atac.nodup_bams"``? : Array of filtered (deduped) BAM file path/URI. - 1st dimension: replicate ID * ``"atac.tas"``? : Array of TAG-ALIGN file path/URI. - 1st dimension: replicate ID * ``"atac.peaks"``? : Array of NARROWPEAK file path/URI. - 1st dimension: replicate ID * ``"atac.peaks_pr1"``? : Array of NARROWPEAK file path/URI for 1st self pseudo replicate of replicate ID. - 1st dimension: replicate ID * ``"atac.peaks_pr2"``? : Array of NARROWPEAK file path/URI for 2nd self pseudo replicate of replicate ID. - 1st dimension: replicate ID * ``"atac.peak_ppr1"``? : NARROWPEAK file path/URI for pooled 1st pseudo replicates. * ``"atac.peak_ppr2"``? : NARROWPEAK file path/URI for pooled 2nd pseudo replicates. * ``"atac.peak_pooled"``? : NARROWPEAK file path/URI for pooled replicate. If starting from peaks then always define ``"atac.peaks"``. Define ``"atac.peaks_pr1"``, ``"atac.peaks_pr2"``, ``"atac.peak_pooled"``, ``"atac.peak_ppr1"`` and ``"atac.peak_ppr2"`` according to the following rules: .. code-block:: javascript if num_rep>1: if true_rep_only: peak_pooled, else: peaks_pr1[], peaks_pr2[], peak_pooled, peak_ppr1, peak_ppr2 else: if true_rep_only: "not the case!" else: peaks_pr1[], peaks_pr2[] #. Pipeline settings Pipeline type (ATAC-Seq or DNase-Seq) : The only difference between two types is TN5 shifting. * ``"atac.pipeline_type`` : ``atac`` for ATAC-Seq. ``dnase`` for DNase-Seq. Input data endedness. * ``"atac.paired_end"`` : Set it as ``true`` if input data are paired end, otherwise ``false``. Other important settings. * ``"atac.align_only"``? : Disable all downstream analysis after mapping. * ``"atac.multimapping"``? : Multimapping reads. * ``"atac.true_rep_only"``? : Set it as ``true`` to disable all analyses (including IDR, naive-overlap and reproducibility QC) related to pseudo replicates. This flag suppresses ``"atac.enable_idr"``. * ``"atac.disable_xcor``? : Disable cross-correlation analysis. #. Adapter trimmer settings Structure/dimension of ``"atac.adapters`` must match with that of ``"atac.fastqs"``. If no adapters are given then do not define ``"atac.adapters"`` in ``input.json``. If some adapters are known then define them in ``"atac.adapters"`` and leave other entries empty (``""``) while keeping the same structure/dimension as in ``"atac.fastqs"``. All undefined/non-empty adapters will be trimmed without auto detection. * ``"atac.trim_adapter.auto_detect_adapter"``? : Set it as ``true`` to automatically detect/trim adapters for empty entries in ``"atac.adapters"``. There will be no auto detection for non-empty entries it. If ``"atac.adapters"`` is not defined then all adapters will be detected/trimmed for all fastqs. * ``"atac.trim_adapter.min_trim_len"``? : Minimum trim length for ``cutadapt -m``. * ``"atac.trim_adapter.err_rate"``? : Maximum allowed adapter error rate for ``cutadapt -e``. #. Bowtie2 settings * ``"atac.bowtie2.score_min"``? : Min. acceptable alignment score function w.r.t read length. #. Filter/dedup (post-alignment) settings * ``"atac.filter.dup_marker"``? : Dup marker. Choose between ``picard`` (default) and ``sambamba``. * ``"atac.filter.mapq_thresh"``? : Threshold for low MAPQ reads removal. * ``"atac.filter.no_dup_removal"``? : No dup reads removal when filtering BAM. #. BAM-2-TAGALIGN settings Pipeline filters out chrM reads by default. * ``"atac.bam2ta.regex_grep_v_ta"``? : Perl-style regular expression pattern to remove matching reads from TAGALIGN (default: ``chrM``). * ``"atac.bam2ta.subsample"``? : Number of reads to subsample TAGALIGN. Subsampled TAGALIGN will be used for all downstream analysis (MACS2, IDR, naive-overlap). #. Cross correlation analysis settings * ``"atac.xcor.subsample"``? : Number of reads to subsample TAGALIGN. Only one end (R1) will be used for cross correlation analysis. This will not affect downstream analysis. #. MACS2 settings **DO NOT DEFINE MACS2 PARAMETERS IN ``"atac.macs2"`` SCOPE**. All MACS2 parameters must be defined in ``"atac"`` scope. * ``"atac.cap_num_peak"``? : Cap number of raw peaks called from MACS2. * ``"atac.pval_thresh"``? : P-value threshold. * ``"atac.smooth_win"``? : Size of smoothing window. #. IDR settings **DO NOT DEFINE IDR PARAMETERS IN ``"atac.idr"`` SCOPE**. All IDR parameters must be defined in ``"atac"`` scope. * ``"atac.enable_idr"``? : Set it as ``true`` to enable IDR on raw peaks. * ``"atac.idr_thresh"``? : IDR threshold. #. ATAQC (annotation based analysis) settings * ``"atac.disable_ataqc"``? : Set it as ``true`` to disable ATAQC. #. Resources **RESOURCES DEFINED IN ``input.json`` ARE PER TASK**. For example, if you have FASTQs for 2 replicates (2 tasks) and set ``cpu`` for ``bowtie2`` task as 4 then total number of cpu cores to map FASTQs is 2 x 4 = 8. CPU (``cpu``), memory (``mem_mb``) settings are used for submitting jobs to cluster engines (SGE and SLURM) and Cloud platforms (Google Cloud Platform, AWS, ...). VM instance type on cloud platforms will be automatically chosen according to each task's ``cpu`` and ``mem_mb``. Number of cores for tasks without ``cpu`` parameter is fixed at 1. * ``"atac.trim_adapter.cpu"``? : Number of cores for ``trim_adapter`` (default: 2). * ``"atac.bowtie2.cpu"``? : Number of cores for ``bowtie2`` (default: 4). * ``"atac.filter.cpu"``? : Number of cores for ``filter`` (default: 2). * ``"atac.bam2ta.cpu"``? : Number of cores for ``bam2ta`` (default: 2). * ``"atac.xcor.cpu"``? : Number of cores for ``xcor`` (default: 2). * ``"atac.trim_adapter.mem_mb"``? : Max. memory limit in MB for ``trim_adapter`` (default: 10000). * ``"atac.bowtie2.mem_mb"``? : Max. memory limit in MB for ``bowtie2`` (default: 20000). * ``"atac.filter.mem_mb"``? : Max. memory limit in MB for ``filter`` (default: 20000). * ``"atac.bam2ta.mem_mb"``? : Max. memory limit in MB for ``bam2ta`` (default: 10000). * ``"atac.spr.mem_mb"``? : Max. memory limit in MB for ``spr`` (default: 12000). * ``"atac.xcor.mem_mb"``? : Max. memory limit in MB for ``xcor`` (default: 10000). * ``"atac.macs2_mem_mb"``? : Max. memory limit in MB for ``macs2`` (default: 16000). Disks (``disks``) is used for Cloud platforms (Google Cloud Platforms, AWS, ...). * ``"atac.trim_adapter.disks"``? : Disks for ``trim_adapter`` (default: "local-disk 100 HDD"). * ``"atac.bowtie2.disks"``? : Disks for ``bowtie2`` (default: "local-disk 100 HDD"). * ``"atac.filter.disks"``? : Disks for ``filter`` (default: "local-disk 100 HDD"). * ``"atac.bam2ta.disks"``? : Disks for ``bam2ta`` (default: "local-disk 100 HDD"). * ``"atac.xcor.disks"``? : Disks for ``xcor`` (default: "local-disk 100 HDD"). * ``"atac.macs2_disks"``? : Disks for ``macs2`` (default: "local-disk 100 HDD"). Walltime (``time``) settings (for SGE and SLURM only). * ``"atac.trim_adapter.time_hr"``? : Walltime for ``trim_adapter`` (default: 24). * ``"atac.bowtie2.time_hr"``? : Walltime for ``bowtie2`` (default: 48). * ``"atac.filter.time_hr"``? : Walltime for ``filter`` (default: 24). * ``"atac.bam2ta.time_hr"``? : Walltime for ``bam2ta`` (default: 6). * ``"atac.xcor.time_hr"``? : Walltime for ``xcor`` (default: 6). * ``"atac.macs2_time_hr"``? : Walltime for ``macs2`` (default: 24). #. QC report HTML/JSON * ``"atac.qc_report.name"``? : Name of sample. * ``"atac.qc_report.desc"``? : Description for sample.