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mmassaviol
WAWmassaviol
Commits
4a706151
Commit
4a706151
authored
Oct 18, 2021
by
abensaid
Browse files
Merge branch 'master' into squeezemeta
parents
95617d8a
7cd140c9
Changes
8
Hide whitespace changes
Inline
Side-by-side
raw_inputs/raw_hisat2_index.py
0 → 100755
View file @
4a706151
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
raw_inputs/raw_hisat2_index.yaml
0 → 100755
View file @
4a706151
{
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
tools/deseq2/deseq2.script.R
View file @
4a706151
...
...
@@ -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
)
}
}
tools/deseq2/deseq2.yaml
View file @
4a706151
...
...
@@ -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"
...
...
tools/fastp/fastp.rule.snakefile
View file @
4a706151
...
...
@@ -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 "",
...
...
tools/global.yaml
View file @
4a706151
...
...
@@ -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"
},
...
...
tools/hisat2/hisat2.rule.snakefile
View file @
4a706151
...
...
@@ -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
...
...
tools/hisat2/hisat2.yaml
View file @
4a706151
...
...
@@ -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
,
...
...
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