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Fix mem sort for HISAT2 output #158

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merged 12 commits into from
Feb 28, 2019
Merged

Fix mem sort for HISAT2 output #158

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59eb9d3
Fix samtools sort taking too much memory
apeltzer Feb 18, 2019
dbf783a
Fix memory issues with hisat2 sorting
apeltzer Feb 18, 2019
52bef54
Fix avail_mem usage hopefully
apeltzer Feb 18, 2019
3663260
Deduct - 100000000 to fix memory issues hopefully
apeltzer Feb 18, 2019
92e53ee
remove the -m part
apeltzer Feb 18, 2019
63354e1
Increase deduction
apeltzer Feb 19, 2019
1f8de20
use more cores (1 i/o, 4 sorting)
apeltzer Feb 22, 2019
60e6574
Use safer defaults
apeltzer Feb 22, 2019
0d8da06
Revert to using 4 cpus
apeltzer Feb 22, 2019
3bdfa9f
Better 5 down
apeltzer Feb 22, 2019
a05c5bf
Use 6GB down
apeltzer Feb 22, 2019
afb19ad
Add check for enough memory to hisat2sort
apeltzer Feb 25, 2019
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@

#### Bug fixes
* Fixing HISAT2 Index Building for large reference genomes [#153](https://github.com/nf-core/rnaseq/issues/153)
* Fixing HISAT2 BAM sorting using more memory than available on the system


#### Dependency Updates
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5 changes: 3 additions & 2 deletions main.nf
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Expand Up @@ -671,11 +671,12 @@ if(params.aligner == 'hisat2'){
file "where_are_my_files.txt"

script:
def avail_mem = task.memory ? "-m ${task.memory.toBytes() / task.cpus}" : ''
def suff_mem = ("${(task.memory.toBytes() - 6000000000) / task.cpus}" > 2000000000) ? 'true' : 'false'
def avail_mem = (task.memory && suff_mem) ? "-m" + "${(task.memory.toBytes() - 6000000000) / task.cpus}" : ''
"""
samtools sort \\
$hisat2_bam \\
-@ ${task.cpus} $avail_mem \\
-@ ${task.cpus} ${avail_mem} \\
-o ${hisat2_bam.baseName}.sorted.bam
samtools index ${hisat2_bam.baseName}.sorted.bam
"""
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