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LBMC
Hub
hic
Commits
56fe1c1d
Commit
56fe1c1d
authored
4 years ago
by
nservant
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[MODIF] fix bugs
parent
e51d04fe
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2
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2 changed files
main.nf
+11
-11
11 additions, 11 deletions
main.nf
nextflow.config
+5
-2
5 additions, 2 deletions
nextflow.config
with
16 additions
and
13 deletions
main.nf
+
11
−
11
View file @
56fe1c1d
...
...
@@ -274,7 +274,7 @@ if (params.res_dist_decay){
// Resolutions for contact maps
map_res
=
Channel
.
from
(
params
.
bin_size
).
splitCsv
().
flatten
()
map_res
.
concat
(
comp_bin
,
tads_bin
,
ddecay_bin
)
map_res
.
concat
(
tads_bin
,
ddecay_bin
)
.
unique
()
.
set
{
map_res
}
...
...
@@ -831,9 +831,8 @@ process build_contact_maps{
file
chrsize
from
chromosome_size
.
collect
()
output:
file
(
"*.matrix"
)
into
raw_maps
,
raw_maps_4cool
file
"*.bed"
set
val
(
sample
),
val
(
mres
),
file
(
"*.matrix"
),
file
(
"*.bed"
)
into
raw_maps
,
raw_maps_4cool
script:
"""
build_matrix --matrix-format upper --binsize ${mres} --chrsizes ${chrsize} --ifile ${vpairs} --oprefix ${sample}_${mres}
...
...
@@ -853,11 +852,11 @@ process run_ice{
!
params
.
skip_maps
&&
!
params
.
skip_ice
input:
file
(
rmaps
)
from
raw_maps
file
"*.biases"
set
val
(
sample
),
val
(
res
),
file
(
rmaps
),
file
(
bed
)
from
raw_maps
output:
file
(
"*iced.matrix"
)
into
iced_maps_4h5
,
iced_maps_4cool
set
val
(
sample
),
val
(
res
),
file
(
"*iced.matrix"
),
file
(
bed
)
into
iced_maps_4h5
,
iced_maps_4cool
file
(
"*.biases"
)
into
iced_bias
script:
prefix
=
rmaps
.
toString
()
-
~
/(\.matrix)?$/
...
...
@@ -884,10 +883,10 @@ process convert_to_cool {
input:
set
val
(
sample
),
val
(
res
),
file
(
mat
),
file
(
bed
)
from
iced_maps_4cool
file
chrsize
from
chrsize_cool
.
collect
()
file
chrsize
from
chr
omosome_
size_cool
.
collect
()
output:
set
val
(
sample
),
val
(
res
),
file
(
"*cool"
)
into
cool_maps
set
val
(
sample
),
val
(
res
),
file
(
"*
.
cool"
)
into
cool_maps
file
(
"*.mcool"
)
into
mcools_maps
script:
...
...
@@ -993,6 +992,7 @@ process tads_hicexplorer {
chIS
=
cool_maps
.
combine
(
tads_res_insulation
).
filter
{
it
[
1
]
==
it
[
3
]
}.
dump
(
tag
:
"ins"
)
/*
process tads_insulation {
tag "$sample - $res"
label 'process_medium'
...
...
@@ -1012,7 +1012,7 @@ process tads_insulation {
cooltools diamond-insulation --window-pixels ${cool} 15 25 50 > ${sample}_insulation.tsv
"""
}
*/
/*
...
...
@@ -1131,7 +1131,7 @@ workflow.onComplete {
def
email_html
=
html_template
.
toString
()
// Render the sendmail template
def
smail_fields
=
[
email:
email_address
,
subject:
subject
,
email_txt:
email_txt
,
email_html:
email_html
,
base
Dir:
"$projectDir"
,
mqcFile:
mqc_report
,
mqcMaxSize:
params
.
max_multiqc_email_size
.
toBytes
()
]
def
smail_fields
=
[
email:
email_address
,
subject:
subject
,
email_txt:
email_txt
,
email_html:
email_html
,
project
Dir:
"$projectDir"
,
mqcFile:
mqc_report
,
mqcMaxSize:
params
.
max_multiqc_email_size
.
toBytes
()
]
def
sf
=
new
File
(
"$projectDir/assets/sendmail_template.txt"
)
def
sendmail_template
=
engine
.
createTemplate
(
sf
).
make
(
smail_fields
)
def
sendmail_html
=
sendmail_template
.
toString
()
...
...
This diff is collapsed.
Click to expand it.
nextflow.config
+
5
−
2
View file @
56fe1c1d
...
...
@@ -66,13 +66,16 @@ params {
ice_eps
=
0
.
1
//
Downstream
Analysis
res_dist_decay
=
1000000
res_tads
=
40000
,
20000
res_dist_decay
=
'1000000'
tads_caller
=
"hicexplorer,insulation"
res_tads
=
'40000,20000'
//
Workflow
skip_maps
=
false
skip_ice
=
false
skip_cool
=
false
skip_dist_decay
=
false
skip_tads
=
false
skip_multiqc
=
false
//
Boilerplate
options
...
...
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Click to expand it.
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