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Christian Arnold
ATACSeq_Snakemake
Commits
a1da775e
Commit
a1da775e
authored
4 years ago
by
Christian Arnold
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Changes to cluster.json
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aa605743
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example/templates/cluster.json
+29
-29
29 additions, 29 deletions
example/templates/cluster.json
with
29 additions
and
29 deletions
example/templates/cluster.json
+
29
−
29
View file @
a1da775e
...
...
@@ -3,7 +3,7 @@
"queueSLURM"
:
"htc"
,
"group"
:
"zaugg"
,
"nCPUs"
:
"{threads}"
,
"memory"
:
1
0000
,
"memory"
:
2
0000
,
"nodes"
:
"avx2"
,
"maxTime"
:
"5:00:00"
,
"qos"
:
"normal"
,
...
...
@@ -13,19 +13,19 @@
"willBeIgnored_canBeDeleted"
:
"SEE ALSO BELOW IN THE RULES FOR MORE OCCURENCES OF OUTPUT AND ERROR FILES TO BE REPLACED"
},
"fastqc_BT"
:
{
"memory"
:
5
000
,
"memory"
:
10
000
,
"maxTime"
:
"2:00:00"
},
"trimming_PE"
:
{
"memory"
:
5
000
,
"memory"
:
10
000
,
"maxTime"
:
"10:00:00"
},
"fastqc_AT"
:
{
"memory"
:
5
000
,
"memory"
:
10
000
,
"maxTime"
:
"2:00:00"
},
"Bowtie2_alignment"
:
{
"memory"
:
1
5000
,
"memory"
:
2
5000
,
"maxTime"
:
"24:00:00"
},
"samtools_SAM_TO_BAM"
:
{
...
...
@@ -33,15 +33,15 @@
"maxTime"
:
"5:00:00"
},
"Picard_cleanSAM"
:
{
"memory"
:
5
000
,
"memory"
:
20
000
,
"maxTime"
:
"5:00:00"
},
"Picard_FixMateInformation"
:
{
"memory"
:
1
5000
,
"memory"
:
2
5000
,
"maxTime"
:
"5:00:00"
},
"Picard_AddOrReplaceReadGroups"
:
{
"memory"
:
5
000
,
"memory"
:
10
000
,
"maxTime"
:
"5:00:00"
},
"Picard_ReorderSam"
:
{
...
...
@@ -65,7 +65,7 @@
"maxTime"
:
"10:00:00"
},
"postalign_remove_chrMAndUnassembledChr"
:
{
"memory"
:
1000
,
"memory"
:
1000
0
,
"maxTime"
:
"5:00:00"
},
"markDuplicates_Picardtools"
:
{
...
...
@@ -73,31 +73,31 @@
"maxTime"
:
"10:00:00"
},
"computeLibraryComplexity"
:
{
"memory"
:
1000
,
"memory"
:
1000
0
,
"maxTime"
:
"2:00:00"
},
"removeDuplicates"
:
{
"memory"
:
1000
,
"memory"
:
1000
0
,
"maxTime"
:
"5:00:00"
},
"postalign_MAPQ"
:
{
"memory"
:
1000
,
"memory"
:
1000
0
,
"maxTime"
:
"5:00:00"
},
"postaling_RSS"
:
{
"memory"
:
1000
,
"memory"
:
1000
0
,
"maxTime"
:
"5:00:00"
},
"Picard_sortFinal"
:
{
"memory"
:
5
000
,
"memory"
:
10
000
,
"maxTime"
:
"5:00:00"
},
"Picard_cleanSamFinal"
:
{
"memory"
:
5
000
,
"memory"
:
20
000
,
"maxTime"
:
"5:00:00"
},
"Picard_FixMateInformationFinal"
:
{
"memory"
:
1
5000
,
"memory"
:
2
5000
,
"maxTime"
:
"5:00:00"
},
"Picardtools_MergeSamFiles"
:
{
...
...
@@ -105,27 +105,27 @@
"maxTime"
:
"5:00:00"
},
"deepTools_computeGCBias"
:
{
"memory"
:
5
000
,
"memory"
:
10
000
,
"maxTime"
:
"10:00:00"
},
"deepTools_correctGCBias"
:
{
"memory"
:
5
000
,
"memory"
:
10
000
,
"maxTime"
:
"10:00:00"
},
"macs2_stringent"
:
{
"memory"
:
5
000
,
"memory"
:
10
000
,
"maxTime"
:
"10:00:00"
},
"macs2_nonStringent"
:
{
"memory"
:
5
000
,
"memory"
:
10
000
,
"maxTime"
:
"10:00:00"
},
"macs2_Encode"
:
{
"memory"
:
5
000
,
"memory"
:
10
000
,
"maxTime"
:
"10:00:00"
},
"filterPeaks"
:
{
"memory"
:
5
000
,
"memory"
:
10
000
,
"maxTime"
:
"2:00:00"
,
"output"
:
"/YOUR_DIRECTORY/output/LOGS_AND_BENCHMARKS/{rule}.out"
,
"error"
:
"/YOUR_DIRECTORY/output/LOGS_AND_BENCHMARKS/{rule}.err"
...
...
@@ -141,7 +141,7 @@
"maxTime"
:
"5:00:00"
},
"stats"
:
{
"memory"
:
5
000
,
"memory"
:
10
000
,
"maxTime"
:
"10:00:00"
},
"bamCoverage"
:
{
...
...
@@ -150,19 +150,19 @@
},
"deepTools_plotCoverage"
:
{
"memory"
:
10000
,
"maxTime"
:
"2
4
:00:00"
"maxTime"
:
"
7
2:00:00"
},
"deepTools_plotCoverageMerged"
:
{
"memory"
:
10000
,
"maxTime"
:
"2
4
:00:00"
"maxTime"
:
"
7
2:00:00"
},
"deepTools_correlationPlots"
:
{
"memory"
:
10000
,
"maxTime"
:
"2
4
:00:00"
"maxTime"
:
"
7
2:00:00"
},
"deepTools_correlationPlotsPooledSamples"
:
{
"memory"
:
10000
,
"maxTime"
:
"2
4
:00:00"
"maxTime"
:
"
7
2:00:00"
},
"deepTools_plotPCA_peaksOnly"
:
{
"memory"
:
10000
,
...
...
@@ -174,7 +174,7 @@
},
"deepTools_correlationPlotsPeaks"
:
{
"memory"
:
10000
,
"maxTime"
:
"
10
:00:00"
"maxTime"
:
"
72
:00:00"
},
"PCA_R"
:
{
"memory"
:
10000
,
...
...
@@ -182,6 +182,6 @@
},
"multiqc"
:
{
"memory"
:
10000
,
"maxTime"
:
"
2
:00:00"
"maxTime"
:
"
5
:00:00"
}
}
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