Commit 4a706151 authored by abensaid's avatar abensaid
Browse files

Merge branch 'master' into squeezemeta

parents 95617d8a 7cd140c9
import os
import re
import sys
def raw_hisat2_index(results_dir, hisat2_index):
out = dict()
from os import listdir
from os.path import isfile, join
onlyfiles = [join( hisat2_index, f) for f in listdir(hisat2_index) if isfile(join(hisat2_index, f))]
out["hisat2_index"] = onlyfiles
return(out)
#print(raw_hisat2_index(sys.argv[1],sys.argv[2])
\ No newline at end of file
{
name: raw_hisat2_index,
function_call: "raw_hisat2_index(config['results_dir'], config['hisat2_index'])",
options: [
{
name: "hisat2_index",
type: "input_dir",
value: "/Data",
label: "Directory containing the hisat2 index files: ",
volumes: [Data: "/Data", Results: "/Results"]
}
]
}
\ No newline at end of file
......@@ -141,6 +141,7 @@ speciesData = snakemake@params[["biomaRtDataset"]]
#what if we have tarnscript ID or not ENSEMBL ID instead of gene ID ?????????
if we know speciesData make a blast
if (speciesData != "None") {
# Add annotation with biomaRt
library(biomaRt)
......@@ -175,7 +176,8 @@ if (speciesData != "None") {
user_threshold = 0.05, correction_method = "g_SCS",
domain_scope = "annotated", custom_bg = NULL,
numeric_ns = "", sources = sources, as_short_link = FALSE)
if ( nrow(gostres$result) > 1) # we have some results
{
png(filename = paste0(snakemake@params[["outDir"]],"/gprofiler2_plot_mqc.png"), height=800, width=800)
p <- gostplot(gostres, capped = FALSE, interactive = FALSE)
print(p + ggtitle("gprofiler2 enrichment analysis for top genes to find over-representation of terms from Gene Ontology"))
......@@ -188,7 +190,7 @@ if (speciesData != "None") {
ttable = cbind(1:nrow(gostres$result), gostres$result[,-14])
colnames(ttable)[1]="id"
write.table(ttable, paste0(snakemake@params[["outDir"]],"/gprofiler2_mqc.tsv"), sep="\t",row.names =FALSE, quote = FALSE)
}
}
......@@ -62,7 +62,7 @@
Mus musculus: "mmusculus_gene_ensembl",
Homo sapiens: "hsapiens_gene_ensembl",
Nile tilapia: "oniloticus_gene_ensembl",
oniloticus_gene_ensembl: "dmelanogaster_gene_ensembl"
Drosophila melanogaster: "dmelanogaster_gene_ensembl"
],
value: "None",
label: "Species"
......
......@@ -11,7 +11,7 @@ if config["SeOrPe"] == "PE":
params:
command = config["<step_name>__fastp_PE_command"],
complexity_threshold = config["<step_name>__fastp_complexity_threshold"],
report_title = config["<step_name>__fastp_report_title"]+" : "+{sample},
report_title = config["<step_name>__fastp_report_title"]+" : {sample}",
detect_adapter_for_pe = "--detect_adapter_for_pe" if config["<step_name>__fastp_adapter_detection_PE"] == True else "",
adapter_sequence = "--adapter_sequence "+config["<step_name>__fastp_adapter_sequence"] if config["<step_name>__fastp_adapter_sequence"] != "" else "",
adapter_sequence_R2 = "--adapter_sequence_r2 " + config["<step_name>__fastp_adapter_sequence_R2_PE"] if config["<step_name>__fastp_adapter_sequence_R2_PE"] != "" else "",
......
......@@ -55,6 +55,7 @@ data: [
{name: "bowtie_index", category: "index"},
{name: "bowtie2_index", category: "index"},
{name: "bwa_mem_index", category: "index"},
{name: "hisat2_index", category: "index"},
{name: "bwa_mem_2_index", category: "index"},
{name: "kallisto_index", category: "index"},
{name: "salmon_index", category: "index"},
......
......@@ -14,15 +14,15 @@ if config["SeOrPe"] == "PE":
#indexPrefix = config["<step_name>__hisat2_index_output_dir"]+"/index",
#here we have index files : from .1.ht2 to .8.ht2
indexPrefix = lambda w, input: os.path.splitext(os.path.splitext([x for x in input.index ][0])[0])[0],
minins = config["<step_name>__hisat2_minins_PE"],
maxins = config["<step_name>__hisat2_maxins_PE"],
minins = "-I " + config["<step_name>__hisat2_minins_PE"] if config["<step_name>__hisat2_reads_type"] == "genome" else "",
maxins = "-X " + config["<step_name>__hisat2_maxins_PE"] if config["<step_name>__hisat2_reads_type"] == "genome" else "",
orientation = config["<step_name>__hisat2_orientation_PE"],
shell:
"{params.command} --new-summary "
"--threads {threads} "
"-x {params.indexPrefix} "
"-I {params.minins} "
"-X {params.maxins} "
"{params.minins} "
"{params.maxins} "
"{params.orientation} "
"--rg-id ID:WAW --rg SM:{wildcards.sample} "
#"-S "#output in sam format
......
......@@ -20,6 +20,17 @@
outputs: [{ name: bam, type: "bams", file: "{sample}.bam", description: "Alignment files" }],
options:
[
{
name: hisat2_reads_type,
type: radio,
choices:
[
genome: "genome",
transcriptome: "transcriptome",
],
value: "transcriptome",
label: "Type of reads sequences",
},
{
name: hisat2_threads,
prefix: --threads,
......@@ -30,6 +41,13 @@
step: 1,
label: "Number of threads to use to align reads",
},
{
name: templatelen_adjustment,
prefix: --no-templatelen-adjustment,
type: "checkbox",
value: TRUE,
label: "Disables template length adjustment for RNA-seq reads",
},
{
name: hisat2_minins_PE,
prefix: -I,
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment