Mercurial > repos > iuc > scpipe

annotate scpipe.R @ 3:7397e6badc11 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
author iuc
date Thu, 11 Jun 2020 07:18:37 -0400
parents 5c4bca9dd4a2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
1 err_foo <- function() {
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
2 cat(geterrmessage(), file = stderr());
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
3 q("no", 1, F)
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
4 }
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
5 options(show.error.messages = F, error = err_foo)
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
6
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
7 # we need that to not crash galaxy with an UTF8 error on German LC settings.
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
8 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
9
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
10 suppressPackageStartupMessages({
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
11 library(scPipe)
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
12 library(SingleCellExperiment)
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
13 library(optparse)
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
14 library(readr)
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
15 library(ggplot2)
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
16 library(plotly)
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
17 library(DT)
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
18 library(scater)
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
19 library(scran)
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
20 library(scales)
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
21 library(Rtsne)
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
22 })
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
23
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
24 option_list <- list(
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
25 make_option(c("-bam", "--bam"), type = "character", help = "BAM file"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
26 make_option(c("-fasta", "--fasta"), type = "character", help = "Genome fasta file"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
27 make_option(c("-exons", "--exons"), type = "character", help = "Exon annotation gff3 file"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
28 make_option(c("-organism", "--organism"), type = "character", help = "Organism e.g. hsapiens_gene_ensembl"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
29 make_option(c("-barcodes", "--barcodes"), type = "character", help = "Cell barcodes csv file"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
30 make_option(c("-read1", "--read1"), type = "character", help = "Read 1 fastq.gz"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
31 make_option(c("-read2", "--read2"), type = "character", help = "Read 2 fastq.gz"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
32 make_option(c("-samplename", "--samplename"), type = "character", help = "Name to use for sample"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
33 make_option(c("-bs1", "--bs1"), type = "integer", help = "Barcode start in Read 1"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
34 make_option(c("-bl1", "--bl1"), type = "integer", help = "Barcode length in Read 1"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
35 make_option(c("-bs2", "--bs2"), type = "integer", help = "Barcode start in Read 2"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
36 make_option(c("-bl2", "--bl2"), type = "integer", help = "Barcode length in Read 2"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
37 make_option(c("-us", "--us"), type = "integer", help = "UMI start in Read 2"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
38 make_option(c("-ul", "--ul"), type = "integer", help = "UMI length in Read 2"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
39 make_option(c("-rmlow", "--rmlow"), type = "logical", help = "Remove reads with N in barcode or UMI"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
40 make_option(c("-rmN", "--rmN"), type = "logical", help = "Remove reads with low quality"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
41 make_option(c("-minq", "--minq"), type = "integer", help = "Minimum read quality"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
42 make_option(c("-numbq", "--numbq"), type = "integer", help = "Maximum number of bases below minq"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
43 make_option(c("-stnd", "--stnd"), type = "logical", help = "Perform strand-specific mapping"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
44 make_option(c("-max_mis", "--max_mis"), type = "integer", help = "Maximum mismatch allowed in barcode"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
45 make_option(c("-UMI_cor", "--UMI_cor"), type = "integer", help = "Correct UMI sequence error"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
46 make_option(c("-gene_fl", "--gene_fl"), type = "logical", help = "Remove low abundant genes"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
47 make_option(c("-max_reads", "--max_reads"), type = "integer", help = "Maximum reads processed"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
48 make_option(c("-min_count", "--min_count"), type = "integer", help = "Minimum count to keep"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
49 make_option(c("-metrics_matrix", "--metrics_matrix"), type = "logical", help = "QC metrics matrix"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
50 make_option(c("-keep_outliers", "--keep_outliers"), type = "logical", help = "Keep outlier cells"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
51 make_option(c("-report", "--report"), type = "logical", help = "HTML report of plots"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
52 make_option(c("-rdata", "--rdata"), type = "logical", help = "Output RData file"),
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
53 make_option(c("-nthreads", "--nthreads"), type = "integer", help = "Number of threads")
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
54 )
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
55
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
56 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
57 args <- parse_args(parser)
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
58
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
59 bam <- args$bam
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
60 fa_fn <- args$fasta
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
61 anno_fn <- args$exons
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
62 fq_r1 <- args$read1
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
63 fq_r2 <- args$read2
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
64 read_structure <- list(bs1 = args$bs1, # barcode start position in fq_r1, -1 indicates no barcode
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
65 bl1 = args$bl1, # barcode length in fq_r1, 0 since no barcode present
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
66 bs2 = args$bs2, # barcode start position in fq_r2
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
67 bl2 = args$bl2, # barcode length in fq_r2
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
68 us = args$us, # UMI start position in fq_r2
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
69 ul = args$ul # UMI length
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
70 )
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
71
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
72 if (args$us == -1) {
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
73 has_umi <- FALSE
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
74 } else {
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
75 has_umi <- TRUE
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
76 }
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
77
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
78 filter_settings <- list(rmlow = args$rmlow,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
79 rmN = args$rmN,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
80 minq = args$minq,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
81 numbq = args$numbq)
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
82
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
83 # Outputs
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
84 out_dir <- "."
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
85 mapped_bam <- file.path(out_dir, "aligned.mapped.bam")
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
86
2
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
87 # if input is fastqs
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
88 if (!is.null(fa_fn)) {
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
89 fasta_index <- file.path(out_dir, paste0(fa_fn, ".fasta_index"))
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
90 combined_fastq <- file.path(out_dir, "combined.fastq")
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
91 aligned_bam <- file.path(out_dir, "aligned.bam")
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
92
2
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
93 print("Trimming barcodes")
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
94 sc_trim_barcode(combined_fastq,
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
95 fq_r1,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
96 fq_r2,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
97 read_structure = read_structure,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
98 filter_settings = filter_settings)
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
99
2
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
100 print("Building genome index")
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
101 Rsubread::buildindex(basename = fasta_index, reference = fa_fn)
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
102
2
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
103 print("Aligning reads to genome")
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
104 Rsubread::align(index = fasta_index,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
105 readfile1 = combined_fastq,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
106 output_file = aligned_bam,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
107 nthreads = args$nthreads)
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
108
2
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
109 if (!is.null(args$barcodes)) {
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
110 barcode_anno <- args$barcodes
2
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
111 } else {
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
112 print("Detecting barcodes")
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
113 # detect 10X barcodes and generate sample_index.csv file
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
114 barcode_anno <- "sample_index.csv"
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
115 sc_detect_bc(infq = combined_fastq,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
116 outcsv = barcode_anno,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
117 bc_len = read_structure$bl2,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
118 max_reads = args$max_reads,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
119 min_count = args$min_count,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
120 max_mismatch = args$max_mis
2
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
121 )
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
122 }
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
123 } else {
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
124 aligned_bam <- file.path(out_dir, bam)
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
125 barcode_anno <- args$barcodes
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
126 }
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
127
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
128 print("Assigning reads to exons")
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
129 sc_exon_mapping(aligned_bam, mapped_bam, anno_fn, bc_len = read_structure$bl2, UMI_len = read_structure$ul, stnd = args$stnd)
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
130
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
131 print("De-multiplexing data")
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
132 sc_demultiplex(mapped_bam, out_dir, barcode_anno, has_UMI = has_umi)
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
133
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
134 print("Counting genes")
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
135 sc_gene_counting(out_dir, barcode_anno, UMI_cor = args$UMI_cor, gene_fl = args$gene_fl)
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
136
2
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
137 print("Performing QC")
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
138 sce <- create_sce_by_dir(out_dir)
2
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
139 pdf("plots.pdf")
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
140 plot_demultiplex(sce)
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
141 if (has_umi) {
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
142 p <- plot_UMI_dup(sce)
2
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
143 print(p)
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
144 }
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
145 sce <- calculate_QC_metrics(sce)
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
146 sce <- detect_outlier(sce)
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
147 p <- plot_mapping(sce, percentage = TRUE, dataname = args$samplename)
2
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
148 print(p)
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
149 p <- plot_QC_pairs(sce)
2
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
150 print(p)
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
151 dev.off()
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
152
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
153 print("Removing outliers")
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
154 if (is.null(args$keep_outliers)) {
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
155 sce <- remove_outliers(sce)
2
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
156 gene_counts <- counts(sce)
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
157 write.table(data.frame("gene_id" = rownames(gene_counts), gene_counts), file = "gene_count.tsv", sep = "\t", quote = FALSE, row.names = FALSE)
2
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
158 }
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
159
2
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
160 if (!is.null(args$metrics_matrix)) {
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
161 metrics <- colData(sce, internal = TRUE)
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
162 write.table(data.frame("cell_id" = rownames(metrics), metrics), file = "metrics_matrix.tsv", sep = "\t", quote = FALSE, row.names = FALSE)
2
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
163 }
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
164
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
165 if (!is.null(args$report) & (!is.null(fa_fn))) {
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686
iuc
parents: 0
diff changeset
166 print("Creating report")
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
167 create_report(sample_name = args$samplename,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
168 outdir = out_dir,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
169 r1 = fq_r1,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
170 r2 = fq_r2,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
171 outfq = combined_fastq,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
172 read_structure = read_structure,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
173 filter_settings = filter_settings,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
174 align_bam = aligned_bam,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
175 genome_index = fasta_index,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
176 map_bam = mapped_bam,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
177 exon_anno = anno_fn,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
178 stnd = args$stnd,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
179 fix_chr = FALSE,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
180 barcode_anno = barcode_anno,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
181 max_mis = args$max_mis,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
182 UMI_cor = args$UMI_cor,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
183 gene_fl = args$gene_fl,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
184 organism = args$organism,
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
185 gene_id_type = "ensembl_gene_id")
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
186 }
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
187
3
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
188 if (!is.null(args$rdata)) {
7397e6badc11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8007f71281553ddfa45e6f8e1172952d956bb000"
iuc
parents: 2
diff changeset
189 save(sce, file = file.path(out_dir, "scPipe_analysis.RData"))
0
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
190 }
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
191
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
192 sessionInfo()