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md formatting changes in config
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@emmarousseau
emmarousseau committed Jul 5, 2024
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Showing 1 changed file with 71 additions and 88 deletions.
159 changes: 71 additions & 88 deletions src/umi_tools/umi_tools_dedup/config.vsh.yaml
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Expand Up @@ -22,40 +22,37 @@ argument_groups:
- name: --in_sam
type: boolean_true
description: |
By default, inputs are assumed to be in BAM format. Use this options
to specify the use of SAM format for input.
By default, inputs are assumed to be in BAM format. Use this options to specify the use of SAM
format for input.
- name: --bai
type: file
description: BAM index
- name: --random_seed
type: integer
description: |
Random seed to initialize number generator with.
description: Random seed to initialize number generator with.

- name: Outputs
arguments:
- name: --output
alternatives: --stdout
type: file
description: Deduplicated BAM file
description: Deduplicated BAM file.
required: true
direction: output
- name: --out_sam
type: boolean_true
description: |
By default, outputa are written in BAM format. Use this options to
specify the use of SAM format for output.
By default, outputa are written in BAM format. Use this options to specify the use of SAM format
for output.
- name: --paired
type: boolean_true
description: |
BAM is paired end - output both read pairs. This will also force the
use of the template length to determine reads with the same mapping
coordinates.
BAM is paired end - output both read pairs. This will also force the use of the template length
to determine reads with the same mapping coordinates.
- name: --output_stats
type: string
description: |
Generate files containing UMI based deduplication statistics files with this prefix
in the file names.
Generate files containing UMI based deduplication statistics files with this prefix in the file names.
- name: --extract_umi_method
type: string
choices: [read_id, tag, umis]
Expand All @@ -69,35 +66,30 @@ argument_groups:
- name: --umi_tag
type: string
description: |
The tag containing the UMI sequence.
This is only required if the extract_umi_method is set to tag.
The tag containing the UMI sequence. This is only required if the extract_umi_method is set to tag.
- name: --umi_separator
type: string
description: |
The separator used to separate the UMI from the read sequence.
This is only required if the extract_umi_method is set to id_read. [_]
The separator used to separate the UMI from the read sequence. This is only required if the
extract_umi_method is set to id_read. Default: `_`.
example: '_'
- name: --umi_tag_split
type: string
description: |
Separate the UMI in tag by <SPLIT> and take the first element.
description: Separate the UMI in tag by <SPLIT> and take the first element.
- name: --umi_tag_delimiter
type: string
description: |
Separate the UMI in by <DELIMITER> and concatenate the elements
description: Separate the UMI in by <DELIMITER> and concatenate the elements.
- name: --cell_tag
type: string
description: |
The tag containing the cell barcode sequence.
This is only required if the extract_umi_method is set to tag.
The tag containing the cell barcode sequence. This is only required if the extract_umi_method
is set to tag.
- name: --cell_tag_split
type: string
description: |
Separate the cell barcode in tag by <SPLIT> and take the first element.
description: Separate the cell barcode in tag by <SPLIT> and take the first element.
- name: --cell_tag_delimiter
type: string
description: |
Separate the cell barcode in by <DELIMITER> and concatenate the elements
description: Separate the cell barcode in by <DELIMITER> and concatenate the elements.

- name: Grouping Options
arguments:
Expand All @@ -116,89 +108,80 @@ argument_groups:
- name: --edit_distance_threshold
type: integer
description: |
For the adjacency and cluster methods the threshold for the edit
distance to connect two UMIs in the network can be increased. The
default value of 1 works best unless the UMI is very long (>14bp). [1]
For the adjacency and cluster methods the threshold for the edit distance to connect two
UMIs in the network can be increased. The default value of 1 works best unless the UMI is
very long (>14bp). Default: `1`.
example: 1
- name: --spliced_is_unique
type: boolean_true
description: |
Causes two reads that start in the same position on the same strand
and having the same UMI to be considered unique if one is spliced
and the other is not. (Uses the 'N' cigar operation to test for splicing).
Causes two reads that start in the same position on the same strand and having the same UMI
to be considered unique if one is spliced and the other is not. (Uses the 'N' cigar operation
to test for splicing).
- name: --soft_clip_threshold
type: integer
description: |
Mappers that soft clip will sometimes do so rather than mapping a
spliced read if there is only a small overhang over the exon junction.
By setting this option, you can treat reads with at least this many
bases soft-clipped at the 3' end as spliced. [4]
Mappers that soft clip will sometimes do so rather than mapping a spliced read if there is only
a small overhang over the exon junction. By setting this option, you can treat reads with at
least this many bases soft-clipped at the 3' end as spliced. Default: `4`.
example: 4
- name: --multimapping_detection_method
type: string
description: |
If the sam/bam contains tags to identify multimapping reads, you can
specify for use when selecting the best read at a given loci. Supported
tags are "NH", "X0" and "XT". If not specified, the read with the highest
mapping quality will be selected.
If the sam/bam contains tags to identify multimapping reads, you can specify for use when selecting
the best read at a given loci. Supported tags are `NH`, `X0` and `XT`. If not specified, the read
with the highest mapping quality will be selected.
- name: --read_length
type: boolean_true
description: |
Use the read length as a criteria when deduping, for e.g sRNA-Seq.
description: Use the read length as a criteria when deduping, for e.g. sRNA-Seq.

- name: Single-cell RNA-Seq Options
arguments:
- name: --per_gene
type: boolean_true
description: |
Reads will be grouped together if they have the same gene. This is useful
if your library prep generates PCR duplicates with non identical alignment
positions such as CEL-Seq. Note this option is hardcoded to be on with the
count command. I.e counting is always performed per-gene. Must be combined
with either --gene_tag or --per_contig option.
Reads will be grouped together if they have the same gene. This is useful if your library prep
generates PCR duplicates with non identical alignment positions such as CEL-Seq. Note this option
is hardcoded to be on with the count command. I.e. counting is always performed per-gene. Must be
combined with either --gene_tag or --per_contig option.
- name: --gene_tag
type: string
description: |
Deduplicate per gene. The gene information is encoded in the bam read tag
specified.
Deduplicate per gene. The gene information is encoded in the bam read tag specified.
- name: --assigned_status_tag
type: string
description: |
BAM tag which describes whether a read is assigned to a gene. Defaults to
the same value as given for --gene_tag.
BAM tag which describes whether a read is assigned to a gene. Defaults to the same value as given
for --gene_tag.
- name: --skip_tags_regex
type: string
description: |
Use in conjunction with the --assigned_status_tag option to skip any reads
where the tag matches this regex. Default ("^[__|Unassigned]") matches
anything which starts with "__" or "Unassigned".
Use in conjunction with the --assigned_status_tag option to skip any reads where the tag matches
this regex. Default ("^[__|Unassigned]") matches anything which starts with "__" or "Unassigned".
- name: --per_contig
type: boolean_true
description: |
Deduplicate per contig (field 3 in BAM; RNAME). All reads with the same
contig will be considered to have the same alignment position. This is
useful if you have aligned to a reference transcriptome with one
transcript per gene. If you have aligned to a transcriptome with more
than one transcript per gene, you can supply a map between transcripts
and gene using the --gene_transcript_map option.
Deduplicate per contig (field 3 in BAM; RNAME). All reads with the sam contig will be considered to
have the same alignment position. This is useful if you have aligned to a reference transcriptome
with one transcript per gene. If you have aligned to a transcriptome with more than one transcript
per gene, you can supply a map between transcripts and gene using the --gene_transcript_map option.
- name: --gene_transcript_map
type: file
description: |
A file containing a mapping between gene names and transcript names.
The file should be tab separated with the gene name in the first column
and the transcript name in the second column.
A file containing a mapping between gene names and transcript names. The file should be tab
separated with the gene name in the first column and the transcript name in the second column.
- name: --per_cell
type: boolean_true
description: |
Reads will only be grouped together if they have the same cell barcode.
Can be combined with --per_gene.
Reads will only be grouped together if they have the same cell barcode. Can be combined with
--per_gene.
- name: SAM/BAM Options
arguments:
- name: --mapping_quality
type: integer
description: |
Minimium mapping quality (MAPQ) for a read to be retained. [0]
Minimium mapping quality (MAPQ) for a read to be retained. Default: `0`.
example: 0
- name: --unmapped_reads
type: string
Expand All @@ -217,7 +200,8 @@ argument_groups:
The options are:
* "discard": Discard all chimeric read pairs.
* "use": Deduplicate using read1 only. (default)
* "output": Output chimeric pairs without UMI grouping/deduplication. Only available in umi_tools group.
* "output": Output chimeric pairs without UMI grouping/deduplication. Only available in
umi_tools group.
example: "use"
- name: --unpaired_reads
type: string
Expand All @@ -227,42 +211,38 @@ argument_groups:
The options are:
* "discard": Discard all unmapped reads.
* "use": If read2 is unmapped, deduplicate using read1 only. Requires --paired. (default)
* "output": Output unmapped reads/read pairs without UMI grouping/deduplication. Only available in umi_tools group.
* "output": Output unmapped reads/read pairs without UMI grouping/deduplication. Only available
in umi_tools group.
example: "use"
- name: --ignore_umi
type: boolean_true
description: |
Ignore the UMI and group reads using mapping coordinates only.
description: Ignore the UMI and group reads using mapping coordinates only.
- name: --subset
type: double
description: |
Only consider a fraction of the reads, chosen at random. This is useful
for doing saturation analyses.
Only consider a fraction of the reads, chosen at random. This is useful for doing saturation
analyses.
- name: --chrom
type: string
description: |
Only consider a single chromosome. This is useful for debugging/testing
purposes.
description: Only consider a single chromosome. This is useful for debugging/testing purposes.

- name: Group/Dedup Options
arguments:
- name: --no_sort_output
type: boolean_true
description: |
By default, output is sorted. This involves the use of a temporary unsorted
file (saved in --temp_dir). Use this option to turn off sorting.
By default, output is sorted. This involves the use of a temporary unsorted file (saved in
--temp_dir). Use this option to turn off sorting.
- name: --buffer_whole_contig
type: boolean_true
description: |
Forces dedup to parse an entire contig before yielding any reads for
deduplication. This is the only way to absolutely guarantee that all reads
with the same start position are grouped together for deduplication since
dedup uses the start position of the read, not the alignment coordinate on
which the reads are sorted. However, by default, dedup reads for another
1000bp before outputting read groups which will avoid any reads being missed
with short read sequencing (<1000bp).
Forces dedup to parse an entire contig before yielding any reads for deduplication. This is the
only way to absolutely guarantee that all reads with the same start position are grouped together
for deduplication since dedup uses the start position of the read, not the alignment coordinate on
which the reads are sorted. However, by default, dedup reads for another 1000bp before outputting
read groups which will avoid any reads being missed with short read sequencing (<1000bp).
- name: Common UMI-tools Options
- name: Common Options
arguments:
- name: --log
alternatives: -L
Expand All @@ -274,7 +254,8 @@ argument_groups:
- name: --verbose
alternatives: -v
type: integer
description: Log level. The higher, the more output. [0]
description: |
Log level. The higher, the more output. Default: `0`.
example: 0
- name: --error
alternatives: -E
Expand All @@ -287,14 +268,16 @@ argument_groups:
- name: --compresslevel
type: integer
description: |
Level of Gzip compression to use. Default=6 matches GNU gzip rather than python gzip default. [6]
Level of Gzip compression to use. Default=6 matches GNU gzip rather than python gzip default.
Default: `6`.
example: 6
- name: --timeit
type: file
description: Store timing information in file.
- name: --timeit_name
type: string
description: Name in timing file for this class of jobs. [all]
description: |
Name in timing file for this class of jobs. Default: `all`.
example: "all"
- name: --timeit_header
type: string
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