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cmazzoni
Genome_Evaluation_Pipeline
Commits
fc7d38fa
Commit
fc7d38fa
authored
2 years ago
by
james94
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configuration/define_resources.yaml
+38
-41
38 additions, 41 deletions
configuration/define_resources.yaml
with
38 additions
and
41 deletions
configuration/define_resources.yaml
+
38
−
41
View file @
fc7d38fa
...
@@ -8,63 +8,62 @@
...
@@ -8,63 +8,62 @@
#### PRETEXT ####
#### PRETEXT ####
unzipHiC
_R1
:
unzip
Fastq_R1_
HiC
:
mem_mb
:
500
mem_mb
:
500
0
time
:
"
01:30:05"
time
:
"
01:30:05"
threads
:
4
threads
:
4
unzipHiC
_R2
:
unzip
Fastq_R2_
HiC
:
mem_mb
:
500
mem_mb
:
500
0
time
:
"
01:30:05"
time
:
"
01:30:05"
threads
:
4
threads
:
4
pretext_index_PRI_asm
:
indexFasta_PRI
:
mem_mb
:
72000
mem_mb
:
72000
time
:
"
02:30:00"
time
:
"
02:30:00"
threads
:
1
threads
:
1
pretext_f
astq
2
bam_R1
:
convertF
astq
TO
bam_R1
_HiC
:
mem_mb
:
32000
mem_mb
:
32000
time
:
"
08:00:00"
time
:
"
08:00:00"
threads
:
12
threads
:
12
pretext_f
astq
2
bam_R2
:
convertF
astq
TO
bam_R2
_HiC
:
mem_mb
:
32000
mem_mb
:
32000
time
:
"
08:00:00"
time
:
"
08:00:00"
threads
:
12
threads
:
12
pretext_
filter
_5p
rimeEnd_R1
:
filter
5P
rimeEnd_R1
_HiC
:
mem_mb
:
200
mem_mb
:
200
0
time
:
"
08:00:00"
time
:
"
08:00:00"
threads
:
4
threads
:
4
pretext_
filter
_5p
rimeEnd_R2
:
filter
5P
rimeEnd_R2
_HiC
:
mem_mb
:
200
mem_mb
:
200
0
time
:
"
08:00:00"
time
:
"
08:00:00"
threads
:
4
threads
:
4
p
retext_f
iltered_
combine
:
p
airAndCombineF
iltered_
HiC
:
mem_mb
:
9500
mem_mb
:
9500
time
:
"
08:30:00"
time
:
"
08:30:00"
threads
:
12
threads
:
12
pretext
_m
ap
:
pretext
M
ap
:
mem_mb
:
32000
mem_mb
:
32000
time
:
"
08:30:00"
time
:
"
08:30:00"
threads
:
12
threads
:
12
pretext
_s
napshot
:
pretext
S
napshot
:
mem_mb
:
500
mem_mb
:
500
time
:
"
00:10:00"
time
:
"
00:10:00"
threads
:
1
threads
:
1
unzipFasta_PRI
:
unzipFasta_PRI
:
mem_mb
:
500
mem_mb
:
500
time
:
"
00:15:00"
time
:
"
00:15:00"
...
@@ -90,7 +89,7 @@ busco5:
...
@@ -90,7 +89,7 @@ busco5:
threads
:
16
threads
:
16
g
enome
s
cope2
:
G
enome
S
cope2
Profiles
:
mem_mb
:
500
mem_mb
:
500
time
:
"
00:15:00"
time
:
"
00:15:00"
threads
:
1
threads
:
1
...
@@ -102,20 +101,20 @@ assemblyStats:
...
@@ -102,20 +101,20 @@ assemblyStats:
threads
:
1
threads
:
1
mak
ePDF
:
# ReportWithoutComparisonTables_creat
ePDF:
mem_mb
:
1000
#
mem_mb: 1000
time
:
"
00:10:05"
#
time: "00:10:05"
threads
:
1
#
threads: 1
###### Rules for illuminadb building ##########
###### Rules for illuminadb building ##########
unzipFastq_R1
:
unzipFastq_R1
_illumina
:
mem_mb
:
96000
mem_mb
:
96000
time
:
"
01:45:05"
time
:
"
01:45:05"
threads
:
4
threads
:
4
unzipFastq_R2
:
unzipFastq_R2
_illumina
:
mem_mb
:
96000
mem_mb
:
96000
time
:
"
01:45:05"
time
:
"
01:45:05"
threads
:
4
threads
:
4
...
@@ -123,36 +122,36 @@ unzipFastq_R2:
...
@@ -123,36 +122,36 @@ unzipFastq_R2:
trim10x
b
arcodes
:
trim10x
B
arcodes
_illumina
:
mem_mb
:
500
mem_mb
:
500
0
time
:
"
02:30:05"
time
:
"
02:30:05"
threads
:
4
threads
:
4
trim
Adapters
:
trim
SequencingAdapters_illumina
:
mem_mb
:
500
mem_mb
:
500
0
time
:
"
02:30:05"
time
:
"
02:30:05"
threads
:
8
threads
:
8
fast
qc_I
llumina
:
fast
QC_i
llumina
:
mem_mb
:
1000
mem_mb
:
1000
time
:
"
04:00:05"
time
:
"
04:00:05"
threads
:
4
threads
:
4
meryl
_R1
:
meryl
Count_R1_illumina
:
mem_mb
:
20000
mem_mb
:
20000
time
:
"
01:30:05"
time
:
"
01:30:05"
threads
:
12
threads
:
12
meryl
_R2
:
meryl
Count_R2_illumina
:
mem_mb
:
20000
mem_mb
:
20000
time
:
"
01:30:05"
time
:
"
01:30:05"
threads
:
12
threads
:
12
meryl_illumina
_build
:
meryl
Union
_illumina
:
mem_mb
:
30000
mem_mb
:
30000
time
:
"
02:45:05"
time
:
"
02:45:05"
threads
:
12
threads
:
12
...
@@ -162,35 +161,33 @@ meryl_illumina_build:
...
@@ -162,35 +161,33 @@ meryl_illumina_build:
###### HIFI BUILD #######
###### HIFI BUILD #######
unzip
H
ifi
:
unzip
Fastq_h
ifi
:
mem_mb
:
128000
mem_mb
:
128000
time
:
"
01:30:05"
time
:
"
01:30:05"
threads
:
4
threads
:
4
trimSMRTBellAdapters_hifi
:
mem_mb
:
96000
time
:
"
01:30:05"
threads
:
4
fast
qc
_hifi
:
fast
QC
_hifi
:
mem_mb
:
12000
mem_mb
:
12000
time
:
"
04:00:05"
time
:
"
04:00:05"
threads
:
2
threads
:
2
multi
qc
_hifi
:
multi
QC
_hifi
:
mem_mb
:
4000
mem_mb
:
4000
time
:
"
01:15:05"
time
:
"
01:15:05"
threads
:
2
threads
:
2
meryl_hifi
_count
:
meryl
Count
_hifi
:
mem_mb
:
96000
mem_mb
:
96000
time
:
"
02:30:05"
time
:
"
02:30:05"
threads
:
12
threads
:
12
meryl_hifi
_build
:
meryl
Union
_hifi
:
mem_mb
:
96000
mem_mb
:
96000
time
:
"
01:30:05"
time
:
"
01:30:05"
threads
:
12
threads
:
12
trimSMRTbell
:
mem_mb
:
96000
time
:
"
01:30:05"
threads
:
4
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