Run Chromap to align and preprocess chromatin profiles

This chromap workflow aligns and preprocesses FASTQ data using Chromap.

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Workflow inputs

Below are inputs for chromap workflow. Notice that required inputs are in bold. Options described with [chromap option -…] refer directly to Chromap options and are mentioned in Chromap’s manual.

Name	Description	Example	Default
sample_id	Sample Id.	“shareseq_atac”
genome	Genome reference. It can be either of the following two formats: String. Pre-built genome reference. Google bucket URL of a custom reference, must be a .tar.gz file.	“GRCh38_chromap_v0.1.3”, or “gs://user-bucket/chromap.tar.gz”
input_fastqs_directories	A comma-separated list of input FASTQs directories (urls).	“/path/fastq_dir1,/path/fastq_dir2”
output_directory	GS URL of output directory.	“gs://fc-e0000000-0000-0000-0000-000000000000/chromap_result”
acronym_file	The link/path of an index file in TSV format for fetching preset genome references by their names. Set an GS URI if backend is gcp; an S3 URI for aws backend; an absolute file path for local backend.	“s3://xxxx/index.tsv” or “gs://xxxx/index.tsv”
preset	[chromap option --preset] This option applies multiple options at the same time. It should be applied before other options because options applied later will overwrite the values set by --preset. Available STR are: chip Mapping ChIP-seq reads (-l 2000 --remove-pcr-duplicates --low-mem --BED). atac Mapping ATAC-seq/scATAC-seq reads (-l 2000 --remove-pcr-duplicates --low-mem --trim-adapters --Tn5-shift --remove-pcr-duplicates-at-cell-level --BED). hic Mapping Hi-C reads (-e 4 -q 1 --low-mem --split-alignment --pairs).	“atac” or “hic” or “chip”	“atac”
barcode_whitelist	[chromap option --barcode-whitelist] Cell barcode whitelist file. This is supposed to be a txt file where each line is a whitelisted barcode.
barcode_translate	[chromap option --barcode-translate] Barcode translation file.
read1_fastq_pattern	read 1 Fastq file identifier.	“_S*_L*_R1_001.fastq.gz”	“_S*_L*_R1_001.fastq.gz”
read2_fastq_pattern	read 2 Fastq file identifier.	“_S*_L*_R3_001.fastq.gz”	“_S*_L*_R3_001.fastq.gz”
barcode_fastq_pattern	barcode index Fastq file identifier.	“_S*_L*_R2_001.fastq.gz”	“_S*_L*_R2_001.fastq.gz”
read_format	[chromap option --read-format] Format for read files and barcode files	“r1:0:-1,bc:0:-1”	“r1:0:-1,bc:0:-1”
chromap_version	Chromap version to use. Available options: 0.1.4, 0.1.5.	“0.1.5”	“0.1.5”
split_alignment	[chromap option --split-alignment] Allow split alignments. This option should be set only when mapping Hi-C reads.	False
max_edit_dist_e	[chromap option -e] Max edit distance allowed to map a read.	8	8
min_num_minimizer_s	[chromap option -s] Min number of minimizers required to map a read.	2	2
ignore_minimizer_times_f	[chromap option -f] Skip minimizers occuring > INT1 [500] times. INT2 [1000] is the threshold for a second round of seeding.	“500,1000”	“500,1000”
max_insert_size_l	[chromap option -l] Max insert size, only for paired-end read mapping.	1000	1000
min_mapq_q	[chromap option -q] Min MAPQ in range [0, 60] for mappings to be output.	30	30
min_read_length	[chromap option --min-read-length] Skip mapping the reads of length less than Min read length.	30	30
trim_adaptors	[chromap option --trim-adapters] Try to trim adapters on 3’. This only works for paired-end reads. When the fragment length indicated by the read pair is less than the length of the reads, the two mates are overlapped with each other. Then the regions outside the overlap are regarded as adapters and trimmed.	True
remove_pcr_duplicates	[chromap option --remove-pcr-duplicates] Remove PCR duplicates.	True
remove_pcr_duplicates_at_bulk_level	[chromap option --remove-pcr-duplicates-at-bulk-level] Remove PCR duplicates at bulk level for single cell data.	False
remove_pcr_duplicates_at_cell_level	[chromap option --remove-pcr-duplicates-at-cell-level] Remove PCR duplicates at cell level for single cell data.	False
tn5_shift	[chromap option --Tn5-shift] Perform Tn5 shift. When this option is turned on, the forward mapping start positions are increased by 4bp and the reverse mapping end positions are decreased by 5bp. Note that this works only when –SAM is NOT set.	True
low_mem	[chromap option --low-mem] Use low memory mode. When this option is set, multiple temporary intermediate mapping files might be generated on disk and they are merged at the end of processing to reduce memory usage. When this is NOT set, all the mapping results are kept in the memory before they are saved on disk, which works more efficiently for datasets that are not too large.	True
bc_error_threshold	[chromap option --bc-error-threshold] Max Hamming distance allowed to correct a barcode. Max allowed 2.	1	1
bc_probability_threshold	[chromap option --bc-probability-threshold] Min probability to correct a barcode.	0.9	0.9
output_mappings_not_in_whitelist	[chromap option --output-mappings-not-in-whitelist] Output mappings with barcode not in the whitelist.
output_format	Output format. The following formats are available: bed, tagalign, sam, pairs	“bed”
chr_order	[chromap option --chr-order] File with customized chromsome order.
pairs_natural_chr_order	[chromap option --pairs-natural-chr-order] File with natural chromosome order for pairs flipping.
docker_registry	Docker registry to use: “quay.io/cumulus” for images on Red Hat registry; “cumulusprod” for backup images on Docker Hub.	“quay.io/cumulus”	“quay.io/cumulus”
zones	Google cloud zones to consider for execution.	“us-east1-d us-west1-a us-west1-b”	“us-central1-b”
num_cpu	Number of CPUs to request for mapping, setting chromap option -t.	8	8
memory	Memory size string for count per sample.	“64G”	“64G”
disk_space	Disk space in GB needed for count per sample.	200	200
backend	Cloud infrastructure backend to use. Available options: “gcp” for Google Cloud; “aws” for Amazon AWS; “local” for local machine.	“gcp”	“gcp”
preemptible	Number of maximum preemptible tries allowed. This works only when backend is gcp.	2	2
awsQueueArn	The AWS ARN string of the job queue to be used. This only works for aws backend.	“arn:aws:batch:us-east-1:xxx:job-queue/priority-gwf”	“”

Workflow outputs

See the table below for chromap workflow outputs.

Name	Type	Description
output_aln_directory	String	Google Bucket URL of output directory. Within it, each folder is for one sample in the input sample sheet.

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Prebuilt genome references

We’ve built the following chromap references for users’ convenience:

Keyword	Description
GRCh38_and_mm10_chromap_v0.1.3	Human GRCh38 and Mouse mm10, comparable to cellranger reference GRCh38_and_mm10_atac_v1.2.0
GRCh38_chromap_v0.1.3	Mouse mm10, comparable to cellranger reference GRCh38-2020-A_arc_v2.0.0
mm10_chromap_v0.1.3	Human GRCh38, comparable to cellranger reference mm10-2020-A_arc_v2.0.0