$bds ~/data/software/chipseq_pipeline/chipseq.bds
== chipseq pipeline settings
-type <string> : Type of ChIP-Seq pipeline. TF or histone (default: TF).
-histone <bool> : (LEGACY PARAM) Histone ChIP-Seq. Equivalent to '-type histone'
-final_stage <string> : Final stage for pipeline (bam, filt_bam, tag, xcor and peak).
-sig_trk_for_pooled_rep_only <bool> : Generate MACS2 signal tracks for pooled replicate only.
-aligner <string> : Aligner to map raw reads in FASTQs (default: bwa).
-subsample_xcor <string> : # reads to be subsampled for cross corr. analysis (default: 15M).
-subsample_chip <string> : # reads to subsample exp. replicate. Subsampled tagalign will be used for steps downstream (default: 0; no subsampling).
-subsample <string> : (LEGACY PARAM) # reads to subsample exp. replicate. Subsampled tagalign will be used for steps downstream (default: 0; no subsampling).
-subsample_ctl <string> : # reads to subsample control if non-zero (recommended: 40M or lower).
-anon_filt_bam <bool> : Generate an annomymized filtered bam. This will not affect tasks downsteam.
-peak_caller <string> : Peak caller for IDR analysis (default: spp for TF ChIP-seq and macs2 for Histone ChIP-seq ).
-ctl_depth_ratio <real> : Cut-off ratio of two control tagaligns for pooling (default: 1.2).
-fraglen <int> : (LEGACY PARAM) Manually specify fragment length (default: 0, 0 means parsing fraglen from cross-corr analysis log file).
-idr_rank <string> : Scoring column in narrow peak files for IDR. If not specified, signal.value for SPP peaks (TF) and p.value for MACS2 peaks (histone) are used.
-idr_thresh <real> : IDR threshold : -log_10(score) (default: 0.05).
-use_pooled_ctl <bool> : Force to use pooled control (ignoring criteria to choose control for each replicate).
-true_rep <bool> : Call peaks on true replicates only.
-no_pseudo_rep <bool> : Do not call peaks on self pseudo replicates.
-no_xcor <bool> : Disable cross-correlation analysis.
-no_gpeak_filt <bool> : Disable gapped peak filtering through narrow peak (for histone ChIP-Seq only).
-no_browser_tracks <bool> : Disable generation of genome browser tracks (workaround for bzip2 shared library issue).
-pe_xcor_only <bool> : (PE ONLY) Align R1 of paired end fastqs only and for cross-correlation analysis. All other analyses and QCs will be disabled.
-pe_no_trim_fastq <bool> : (PE ONLY) No fastq trimming and use PE tagAlign for cross-correlation analysis.
-no_jsd <bool> : Disable JSD plot generation
-disable_gb_peak <bool> : Disable gapped/broad peak generation
-no_chipqc <bool> : Disable advanced chipseq qc
== configuration file settings
-c <string> : Configuration file path.
-env <string> : Environment file path.
== parallelization settings
-no_par <bool> : Serialize all tasks (individual tasks can still use multiple threads up to '-nth').
-nth <int> : Maximum # threads for a pipeline. (default: 8).
== cluster/system/resource settings
-wt <string> : Walltime for all single-threaded tasks (example: 8:10:00, 3h, 3600, default: 5h50m, 5:50:00).
-memory <string> : Maximum memory for all single-threaded tasks (equivalent to '-mem', example: 4.5G, 1024M, default: 7G).
-use_system <string> : Force to use a system (equivalent to 'bds -s [SYSTEM_NAME] ...', any system defined in bds.config can be used).
-nice <int> : Set process priority for all tasks (default: 0; -20 (highest) ~ 19 (lowest) ).
-retrial <int> : # of Retrial for failed tasks (default: 0).
-q <string> : Submit tasks to a specified cluster queue.
-unlimited_mem_wt <bool> : Use unlimited max. memory and walltime.
-java_tmp_dir <string> : Java temporary directory. (change it when you get 'Disk quota exceeded' error in Java, default: ${TMPDIR}).
== shell environment settings
-mod <string> : Modules separated by ; (example: "bowtie/2.2.4; bwa/0.7.7; picard-tools/1.92").
-shcmd <string> : Shell commands separated by ;. Shell var. must be written as ${VAR} not as $VAR (example: "export PATH=${PATH}:/usr/test; VAR=test").
-addpath <string> : Path separated by ; or : to be PREPENDED to \$PATH (example: "/bin/test:${HOME}/utils").
-conda_env <string> : Anaconda Python (or Miniconda) environment name for all softwares including Python2.
-conda_env_py3 <string> : Anaconda Python (or Miniconda) environment name for Python3.
-conda_bin_dir <string> : Anaconda Python (or Miniconda) bin directory.
-cluster_task_min_len <int> : Minimum length for a cluster job in seconds (dealing with NFS delayed write, default: 60).
-cluster_task_delay <int> : Constant delay for every job in seconds (dealing with NFS delayed write, default: 0).
== output/title settings
-out_dir <string> : Output directory (default: out).
-title <string> : Prefix for HTML report and outputs without given prefix.
== species settings
-species <string> : Species. need to specify '-species_file' too if you have not installed genome database with 'install_genome_data.sh'.
-species_file <string> : Species file path.
-species_browser <string> : Species name in WashU genome browser.
-ref_fa <string> : Reference genome sequence fasta.
-chrsz <string> : Chromosome sizes file path (use fetchChromSizes from UCSC tools).
-blacklist <string> : Blacklist bed.
-seq_dir <string> : Reference genome sequence directory path (where chr*.fa exist).
== ENCODE accession settings
-ENCODE_accession <string> : ENCODE experiment accession ID (or dataset).
-ENCODE_award_rfa <string> : ENCODE award RFA (e.g. ENCODE3).
-ENCODE_assay_category <string> : ENCODE assay category.
-ENCODE_assay_title <string> : ENCODE assay title.
-ENCODE_award <string> : ENCODE award (e.g. /awards/U41HG007000/).
-ENCODE_lab <string> : Lab (e.g. /labs/anshul-kundaje/)
-ENCODE_assembly <string> : hg19, GRCh38, mm9, mm10.
-ENCODE_alias_prefix <string> : Alias prefix, Alias = alias_prefix: + filename + alias_suffix
-ENCODE_alias_suffix <string> : Alias suffix, Alias = alias_prefix: + filename + alias_suffix
== report settings
-url_base <string> : URL base for output directory.
-viz_genome_coord <string> : WashU genome browser genome coordinate (e.g. chr7:27117661-27153380).
== fastq input definition :
Single-ended : For replicate '-fastq[REP_ID]', For control '-ctl_fastq[REP_ID]'
Paired end : For replicate '-fastq[REP_ID]_[PAIR_ID]', For control '-ctl_fastq[REP_ID]_[PAIR_ID]'
== bam input (raw or filtered) definition :
Raw bam : For replicate '-bam[REP_ID]', For control '-ctl_bam[REP_ID]'.
Filtered bam : For replicate '-filt_bam[REP_ID]', For control '-ctl_filt_bam[REP_ID]'.
== tagalign input definition :
For replicate '-tag[REP_ID]', For control '-ctl_tag[REP_ID]'.
== narrow peak input definition :
For true replicates, use '-peak1' and '-peak2',
For pooled replicates, use '-peak_pooled',
For two PR (self-pseudo-replicates), use '-peak[REP_ID]_pr1' and '-peak[REP_ID]_pr2'
For two PPR (pooled pseudo-replicates), use '-peak_ppr1' and '-peak_ppr2'
== input endedness settings (SE or PE) :
-se <bool> : Singled-ended data set. To specify it for each replicate, '-se[REP_ID]' for exp. reps, '-ctl_se[CTL_ID]' for control.
-pe <bool> : Paired end data set. To specify it for each replicate, '-pe[REP_ID]' for exp. reps, '-ctl_pe[CTL_ID]' for controls.
== align bwa settings (requirements: -bwa_idx)
-param_bwa_aln <string> : Parameters for bwa aln (default: "-q 5 -l 32 -k 2").
-bwa_idx <string> : BWA index (full path prefix of *.bwt file) .
-wt_bwa <string> : Walltime for bwa (default: 47, 47:00:00).
-mem_bwa <string> : Max. memory for bwa (default: 12G).
== fastq trimmer settings
-trim_bp <int> : Number of basepairs after trimming fastqs (default: 50).
== align multimapping settings
-multimapping <int> : # alignments reported for multimapping (default: 0).
== postalign bam settings
-mapq_thresh <int> : Threshold for low MAPQ reads removal (default: 30).
-rm_chr_from_tag <string> : Perl style reg-ex to exclude reads from tag-aligns. (example: 'other|ribo|mito|_', '_', default: blank)
-no_dup_removal <bool> : No dupe removal when filtering raw bam.
-wt_dedup <string> : Walltime for post-alignment filtering (default: 23h, 24:00:00).
-mem_dedup <string> : Max. memory for post-alignment filtering (default: 12G).
-dup_marker <string> : Dup marker for filtering mapped reaads in BAMs: picard or sambamba (default: picard).
-use_sambamba_markdup <bool> : Use sambamba markdup instead of Picard MarkDuplicates (default: false).
== postalign bed/tagalign settings
-mem_shuf <string> : Max. memory for UNIX shuf (default: 12G).
-fraglen0 <bool> : (LEGACY PARAM) Set predefined fragment length as zero for cross corr. analysis (add -speak=0 to run_spp.R).
-speak_xcor <int> : Set user-defined cross-corr. peak strandshift (-speak= in run_spp.R). Use -1 to disable (default: -1).
-extra_param_xcor <string> : Set extra parameters for run_spp.R (cross-corr. analysis only).
-mem_xcor <string> : Max. memory for cross-corr. analysis (default: 15G).
== postalign bed/tagalign settings
-mem_shuf <string> : Max. memory for UNIX shuf (default: 12G).
-fraglen0 <bool> : (LEGACY PARAM) Set predefined fragment length as zero for cross corr. analysis (add -speak=0 to run_spp.R).
-speak_xcor <int> : Set user-defined cross-corr. peak strandshift (-speak= in run_spp.R). Use -1 to disable (default: -1).
-extra_param_xcor <string> : Set extra parameters for run_spp.R (cross-corr. analysis only).
-mem_xcor <string> : Max. memory for cross-corr. analysis (default: 15G).
== callpeak spp settings
-cap_num_peak_spp <string> : Cap number of peaks (-npeak= in run_spp.R) (default: 300000).
-max_ppsize_spp <string> : R stack size (R parameter --max-ppsize=; between 5000 and 5000000) for SPP.
-speak_spp <int> : User-defined cross-corr. peak strandshift (-speak= in run_spp.R). Use -1 to get from upstream cross-corr. analysis (default: -1).
-extra_param_spp <string> : Extra parameters for SPP (run_spp.R, peak calling only).
-wt_spp <string> : Walltime for spp (default: 47h, 47:00:00).
-mem_spp <string> : Max. memory for spp (default: 12G).
== callpeak gem settings
-npeak_gem <int> : Threshold on # of peaks for GEM (default: 300000).
-k_min_gem <int> : Minimum length of k-mers (--k_min in GEM, default: 6).
-k_max_gem <int> : Maximum length of k-mers (--k_max in GEM, default: 13).
-q_val_thresh_gem <real> : Q-value threshold (--q in GEM, default: 0).
-read_dist_gem <string> : Read distribution txt file for GEM (default: $script_dir/etc/Read_Distribution_default.txt).
-extra_param_gem <string> : Extra parameters for GEM.
-wt_gem <string> : Walltime for GEM (default: 47h, 47:00:00).
-mem_gem <string> : Max. memory for GEM (default: 15G).
== callpeak PeakSeq settings
-target_fdr_peakseq <real> : Target FDR for PeakSeq (default: 0.05).
-n_sim_peakseq <int> : Number of simulations for PeakSeq (default: 10).
-enrich_mapped_fraglen_peakseq <int> : Enrichment mapped fragment length for PeakSeq. Use -1 to get from upstream cross-corr. analysis (default: -1).
-min_interpeak_dist_peakseq <int> : Minimum interpeak distance for PeakSeq. Use -1 to get from upstream cross-corr. analysis (default: -1).
-mappability_map_peakseq <string> : Mappability map file for PeakSeq (http://archive.gersteinlab.org/proj/PeakSeq/Mappability_Map).
-max_qval_peakseq <real> : Maximum Q-value for PeakSeq (default: 0.1).
-bckgrnd_model_peakseq <string> : Background model for PeakSeq (default: Simulated).
-extra_param_peakseq <string> : Extra parameters for PeakSeq.
-wt_peakseq <string> : Walltime for PeakSeq (default: 47h, 47:00:00).
-mem_peakseq <string> : Max. memory for PeakSeq (default: 12G).
== callpeak macs2 settings (requirements: -chrsz -gensz)
-gensz <string> : Genome size; hs for human, mm for mouse.
-wt_macs2 <string> : Walltime for MACS2 (default: 23h, 23:00:00).
-mem_macs2 <string> : Max. memory for MACS2 (default: 15G).
-pval_thresh_macs2 <real> : --pvalue for macs2 callpeak (https://github.com/taoliu/MACS#-p--pvalue, default: 0.01)
-keep_dup_macs2 <string> : --keep-dup for macs2 callpeak (https://github.com/taoliu/MACS#--keep-dup, default: all).
-extsize_macs2 <int> : --extsize for macs2 callpeak (https://github.com/taoliu/MACS#--extsize). Use -1 to get from upstream cross-corr. analysis (default: -1).
-shift_macs2 <int> : --shift for macs2 callpeak (https://github.com/taoliu/MACS#--shift, default: 0).
-cap_num_peak_macs2 <string> : Cap number of peaks by taking top N peaks for MACS2 (default: 500K).
-extra_param_macs2 <string> : Extra parameters for macs2 callpeak.
== callpeak naive overlap settings
-nonamecheck <bool> : bedtools intersect -nonamecheck (bedtools>=2.24.0, use this if you get bedtools intersect naming convenction warnings/errors).
== IDR settings
-idr_suffix <bool> : Append IDR threshold to IDR output directory.
== CHIPQC settings
-tss_enrich <string> : TSS enrichment bed for chipqc.
-prom <string> : Promoter bed (promoter region file) for chipqc.
-enh <string> : Enhancer bed (enhancer region file) for chipqc.
-mem_chipqc <string> : Max. memory for CHIPQC (default: 20G).
-wt_chipqc <string> : Walltime for CHIPQC (default: 47h, 47:00:00).