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sc-atac-cluster.cwl
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sc-atac-cluster.cwl
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cwlVersion: v1.0
class: CommandLineTool
requirements:
- class: InlineJavascriptRequirement
- class: EnvVarRequirement
envDef:
R_MAX_VSIZE: $((inputs.vector_memory_limit * 1000000000).toString())
hints:
- class: DockerRequirement
dockerPull: biowardrobe2/sc-tools:v0.0.13
inputs:
query_data_rds:
type: File
inputBinding:
prefix: "--query"
doc: |
Path to the RDS file to load Seurat object from. This file should include
chromatin accessibility information stored in the ATAC assay, as well as
'atac_lsi' and 'atacumap' dimensionality reductions applied to that assay.
dimensions:
type:
- "null"
- int
- int[]
inputBinding:
prefix: "--dimensions"
doc: |
Dimensionality to use when constructing nearest-neighbor graph before clustering
(from 1 to 50). If single value N is provided, use from 2 to N dimensions. If
multiple values are provided, subset to only selected dimensions.
Default: from 2 to 10
cluster_metric:
type:
- "null"
- type: enum
symbols:
- "euclidean"
- "cosine"
- "manhattan"
- "hamming"
inputBinding:
prefix: "--ametric"
doc: |
Distance metric used when constructing nearest-neighbor graph before clustering.
Default: euclidean
cluster_algorithm:
type:
- "null"
- type: enum
symbols:
- "louvain"
- "mult-louvain"
- "slm"
- "leiden"
inputBinding:
prefix: "--algorithm"
doc: |
Algorithm for modularity optimization when running clustering.
Default: slm
resolution:
type:
- "null"
- float
- float[]
inputBinding:
prefix: "--resolution"
doc: |
Clustering resolution applied to the constructed nearest-neighbor graph.
Can be set as an array.
Default: 0.3, 0.5, 1.0
atac_fragments_file:
type: File?
secondaryFiles:
- .tbi
inputBinding:
prefix: "--fragments"
doc: |
Count and barcode information for every ATAC fragment used in the loaded Seurat
object. File should be saved in TSV format with tbi-index file.
genes_of_interest:
type:
- "null"
- string
- string[]
inputBinding:
prefix: "--genes"
doc: |
Genes of interest to build Tn5 insertion frequency plots for the nearest peaks.
If loaded Seurat object includes genes expression information in the RNA assay
it will be additionally shown on the right side of the plots.
Ignored if '--fragments' is not provided.
Default: None
identify_diff_peaks:
type: boolean?
inputBinding:
prefix: "--diffpeaks"
doc: |
Identify differentially accessible peaks between each pair of clusters for all resolutions.
Default: false
minimum_logfc:
type: float?
inputBinding:
prefix: "--logfc"
doc: |
For differentially accessible peaks identification include only those peaks that
on average have log fold change difference in the chromatin accessibility between
every tested pair of clusters not lower than this value. Ignored if '--diffpeaks'
is not set.
Default: 0.25
minimum_pct:
type: float?
inputBinding:
prefix: "--minpct"
doc: |
For differentially accessible peaks identification include only those peaks that
are detected in not lower than this fraction of cells in either of the two tested
clusters. Ignored if '--diffpeaks' is not set.
Default: 0.05
test_to_use:
type:
- "null"
- type: enum
symbols:
- "wilcox"
- "bimod"
- "roc"
- "t"
- "negbinom"
- "poisson"
- "LR"
- "MAST"
- "DESeq2"
inputBinding:
prefix: "--testuse"
doc: |
Statistical test to use for differentially accessible peaks identification.
Ignored if '--diffpeaks' is not set.
Default: LR
export_pdf_plots:
type: boolean?
inputBinding:
prefix: "--pdf"
doc: |
Export plots in PDF.
Default: false
color_theme:
type:
- "null"
- type: enum
symbols:
- "gray"
- "bw"
- "linedraw"
- "light"
- "dark"
- "minimal"
- "classic"
- "void"
inputBinding:
prefix: "--theme"
doc: |
Color theme for all generated plots. One of gray, bw, linedraw, light,
dark, minimal, classic, void.
Default: classic
verbose:
type: boolean?
inputBinding:
prefix: "--verbose"
doc: |
Print debug information.
Default: false
export_h5seurat_data:
type: boolean?
inputBinding:
prefix: "--h5seurat"
doc: |
Save Seurat data to h5seurat file.
Default: false
export_h5ad_data:
type: boolean?
inputBinding:
prefix: "--h5ad"
doc: |
Save Seurat data to h5ad file.
Default: false
export_ucsc_cb:
type: boolean?
inputBinding:
prefix: "--cbbuild"
doc: |
Export results to UCSC Cell Browser. Default: false
output_prefix:
type: string?
inputBinding:
prefix: "--output"
doc: |
Output prefix.
Default: ./sc
parallel_memory_limit:
type: int?
inputBinding:
prefix: "--memory"
doc: |
Maximum memory in GB allowed to be shared between the workers
when using multiple --cpus.
Default: 32
vector_memory_limit:
type: int?
default: 128
doc: |
Maximum vector memory in GB allowed to be used by R.
Default: 128
threads:
type: int?
inputBinding:
prefix: "--cpus"
doc: |
Number of cores/cpus to use.
Default: 1
outputs:
umap_res_plot_png:
type:
- "null"
- type: array
items: File
outputBinding:
glob: "*_umap_res_*.png"
doc: |
Clustered cells UMAP.
PNG format
umap_res_plot_pdf:
type:
- "null"
- type: array
items: File
outputBinding:
glob: "*_umap_res_*.pdf"
doc: |
Clustered cells UMAP.
PDF format
slh_res_plot_png:
type:
- "null"
- type: array
items: File
outputBinding:
glob: "*_slh_res_*.png"
doc: |
Silhouette scores. Downsampled to max 500 cells per cluster.
PNG format
slh_res_plot_pdf:
type:
- "null"
- type: array
items: File
outputBinding:
glob: "*_slh_res_*.pdf"
doc: |
Silhouette scores. Downsampled to max 500 cells per cluster.
PDF format
umap_spl_idnt_res_plot_png:
type:
- "null"
- type: array
items: File
outputBinding:
glob: "*_umap_spl_idnt_res_*.png"
doc: |
Split by dataset clustered cells UMAP.
PNG format
umap_spl_idnt_res_plot_pdf:
type:
- "null"
- type: array
items: File
outputBinding:
glob: "*_umap_spl_idnt_res_*.pdf"
doc: |
Split by dataset clustered cells UMAP.
PDF format
cmp_gr_clst_spl_idnt_res_plot_png:
type:
- "null"
- type: array
items: File
outputBinding:
glob: "*_cmp_gr_clst_spl_idnt_res_*.png"
doc: |
Grouped by cluster split by dataset cells composition plot. Downsampled.
PNG format
cmp_gr_clst_spl_idnt_res_plot_pdf:
type:
- "null"
- type: array
items: File
outputBinding:
glob: "*_cmp_gr_clst_spl_idnt_res_*.pdf"
doc: |
Grouped by cluster split by dataset cells composition plot. Downsampled.
PDF format
cmp_gr_idnt_spl_clst_res_plot_png:
type:
- "null"
- type: array
items: File
outputBinding:
glob: "*_cmp_gr_idnt_spl_clst_res_*.png"
doc: |
Grouped by dataset split by cluster cells composition plot. Downsampled.
PNG format
cmp_gr_idnt_spl_clst_res_plot_pdf:
type:
- "null"
- type: array
items: File
outputBinding:
glob: "*_cmp_gr_idnt_spl_clst_res_*.pdf"
doc: |
Grouped by dataset split by cluster cells composition plot. Downsampled.
PDF format
umap_spl_cnd_res_plot_png:
type:
- "null"
- type: array
items: File
outputBinding:
glob: "*_umap_spl_cnd_res_*.png"
doc: |
Split by grouping condition clustered cells UMAP.
PNG format
umap_spl_cnd_res_plot_pdf:
type:
- "null"
- type: array
items: File
outputBinding:
glob: "*_umap_spl_cnd_res_*.pdf"
doc: |
Split by grouping condition clustered cells UMAP.
PDF format
cmp_gr_clst_spl_cnd_res_plot_png:
type:
- "null"
- type: array
items: File
outputBinding:
glob: "*_cmp_gr_clst_spl_cnd_res_*.png"
doc: |
Grouped by cluster split by condition cells composition plot. Downsampled.
PNG format
cmp_gr_clst_spl_cnd_res_plot_pdf:
type:
- "null"
- type: array
items: File
outputBinding:
glob: "*_cmp_gr_clst_spl_cnd_res_*.pdf"
doc: |
Grouped by cluster split by condition cells composition plot. Downsampled.
PDF format
cmp_gr_cnd_spl_clst_res_plot_png:
type:
- "null"
- type: array
items: File
outputBinding:
glob: "*_cmp_gr_cnd_spl_clst_res_*.png"
doc: |
Grouped by condition split by cluster cells composition plot. Downsampled.
PNG format
cmp_gr_cnd_spl_clst_res_plot_pdf:
type:
- "null"
- type: array
items: File
outputBinding:
glob: "*_cmp_gr_cnd_spl_clst_res_*.pdf"
doc: |
Grouped by condition split by cluster cells composition plot. Downsampled.
PDF format
cvrg_res_plot_png:
type:
- "null"
- type: array
items: File
outputBinding:
glob: "*_cvrg_res_*.png"
doc: |
Tn5 insertion frequency plot around gene.
PNG format
cvrg_res_plot_pdf:
type:
- "null"
- type: array
items: File
outputBinding:
glob: "*_cvrg_res_*.pdf"
doc: |
Tn5 insertion frequency plot around gene.
PDF format
peak_markers_tsv:
type: File?
outputBinding:
glob: "*_peak_markers.tsv"
doc: |
Differentially accessible peaks between each pair of clusters for all resolutions.
TSV format
ucsc_cb_config_data:
type: Directory?
outputBinding:
glob: "*_cellbrowser"
doc: |
Directory with UCSC Cellbrowser configuration data.
ucsc_cb_html_data:
type: Directory?
outputBinding:
glob: "*_cellbrowser/html_data"
doc: |
Directory with UCSC Cellbrowser html data.
ucsc_cb_html_file:
type: File?
outputBinding:
glob: "*_cellbrowser/html_data/index.html"
doc: |
HTML index file from the directory with UCSC Cellbrowser html data.
seurat_data_rds:
type: File
outputBinding:
glob: "*_data.rds"
doc: |
Reduced Seurat data in RDS format
seurat_data_h5seurat:
type: File?
outputBinding:
glob: "*_data.h5seurat"
doc: |
Reduced Seurat data in h5seurat format
seurat_data_h5ad:
type: File?
outputBinding:
glob: "*_data.h5ad"
doc: |
Reduced Seurat data in h5ad format
stdout_log:
type: stdout
stderr_log:
type: stderr
baseCommand: ["sc_atac_cluster.R"]
stdout: sc_atac_cluster_stdout.log
stderr: sc_atac_cluster_stderr.log
$namespaces:
s: http://schema.org/
$schemas:
- https://github.com/schemaorg/schemaorg/raw/main/data/releases/11.01/schemaorg-current-http.rdf
label: "Single-cell ATAC-Seq Cluster Analysis"
s:name: "Single-cell ATAC-Seq Cluster Analysis"
s:alternateName: "Clusters single-cell ATAC-Seq datasets, identifies differentially accessible peaks"
s:downloadUrl: https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/sc-atac-cluster.cwl
s:codeRepository: https://github.com/Barski-lab/workflows
s:license: http://www.apache.org/licenses/LICENSE-2.0
s:isPartOf:
class: s:CreativeWork
s:name: Common Workflow Language
s:url: http://commonwl.org/
s:creator:
- class: s:Organization
s:legalName: "Cincinnati Children's Hospital Medical Center"
s:location:
- class: s:PostalAddress
s:addressCountry: "USA"
s:addressLocality: "Cincinnati"
s:addressRegion: "OH"
s:postalCode: "45229"
s:streetAddress: "3333 Burnet Ave"
s:telephone: "+1(513)636-4200"
s:logo: "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
s:department:
- class: s:Organization
s:legalName: "Allergy and Immunology"
s:department:
- class: s:Organization
s:legalName: "Barski Research Lab"
s:member:
- class: s:Person
s:name: Michael Kotliar
s:email: mailto:[email protected]
s:sameAs:
- id: http://orcid.org/0000-0002-6486-3898
doc: |
Single-cell ATAC-Seq Cluster Analysis
Clusters single-cell ATAC-Seq datasets, identifies differentially
accessible peaks.
s:about: |
usage: sc_atac_cluster.R
[-h] --query QUERY [--dimensions [DIMENSIONS ...]]
[--ametric {euclidean,cosine,manhattan,hamming}]
[--algorithm {louvain,mult-louvain,slm,leiden}]
[--resolution [RESOLUTION ...]] [--fragments FRAGMENTS]
[--genes [GENES ...]] [--diffpeaks] [--logfc LOGFC] [--minpct MINPCT]
[--testuse {wilcox,bimod,roc,t,negbinom,poisson,LR,MAST,DESeq2}]
[--pdf] [--verbose] [--h5seurat] [--h5ad] [--cbbuild] [--output OUTPUT]
[--theme {gray,bw,linedraw,light,dark,minimal,classic,void}]
[--cpus CPUS] [--memory MEMORY]
Single-cell ATAC-Seq Cluster Analysis
options:
-h, --help show this help message and exit
--query QUERY Path to the RDS file to load Seurat object from. This
file should include chromatin accessibility
information stored in the ATAC assay, as well as
'atac_lsi' and 'atacumap' dimensionality reductions
applied to that assay.
--dimensions [DIMENSIONS ...]
Dimensionality to use when constructing nearest-
neighbor graph before clustering (from 1 to 50). If
single value N is provided, use from 2 to N
dimensions. If multiple values are provided, subset to
only selected dimensions. Default: from 2 to 10
--ametric {euclidean,cosine,manhattan,hamming}
Distance metric used when constructing nearest-
neighbor graph before clustering. Default: euclidean
--algorithm {louvain,mult-louvain,slm,leiden}
Algorithm for modularity optimization when running
clustering. Default: slm
--resolution [RESOLUTION ...]
Clustering resolution applied to the constructed
nearest-neighbor graph. Can be set as an array.
Default: 0.3, 0.5, 1.0
--fragments FRAGMENTS
Count and barcode information for every ATAC fragment
used in the loaded Seurat object. File should be saved
in TSV format with tbi-index file.
--genes [GENES ...] Genes of interest to build Tn5 insertion frequency
plots for the nearest peaks. If loaded Seurat object
includes genes expression information in the RNA assay
it will be additionally shown on the right side of the
plots. Ignored if '--fragments' is not provided.
Default: None
--diffpeaks Identify differentially accessible peaks between each
pair of clusters for all resolutions. Default: false
--logfc LOGFC For differentially accessible peaks identification
include only those peaks that on average have log fold
change difference in the chromatin accessibility
between every tested pair of clusters not lower than
this value. Ignored if '--diffpeaks' is not set.
Default: 0.25
--minpct MINPCT For differentially accessible peaks identification
include only those peaks that are detected in not
lower than this fraction of cells in either of the two
tested clusters. Ignored if '--diffpeaks' is not set.
Default: 0.05
--testuse {wilcox,bimod,roc,t,negbinom,poisson,LR,MAST,DESeq2}
Statistical test to use for differentially accessible
peaks identification. Ignored if '--diffpeaks' is not
set. Default: LR
--pdf Export plots in PDF. Default: false
--verbose Print debug information. Default: false
--h5seurat Save Seurat data to h5seurat file. Default: false
--h5ad Save Seurat data to h5ad file. Default: false
--cbbuild Export results to UCSC Cell Browser. Default: false
--output OUTPUT Output prefix. Default: ./sc
--theme {gray,bw,linedraw,light,dark,minimal,classic,void}
Color theme for all generated plots. Default: classic
--cpus CPUS Number of cores/cpus to use. Default: 1
--memory MEMORY Maximum memory in GB allowed to be shared between the
workers when using multiple --cpus. Default: 32