Merge pull request #72 from drpatelh/master

Specify temp dir for sort commands
nf-core · Jan 20, 2020 · 3e7abf0 · 3e7abf0
2 parents 58e979d + e7ea781
commit 3e7abf0
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### `Fixed`
 
 * [#118](https://github.com/nf-core/chipseq/issues/118) - Running on with SGE
+* [#132](https://github.com/nf-core/chipseq/issues/132) - BigWig Error: sort: cannot create temporary file in '': Read-only file system
 * Make executables in `bin/` compatible with Python 3
 
 ### `Dependencies`

diff --git a/main.nf b/main.nf
@@ -966,7 +966,7 @@ process MergedLibBigWig {
     """
     SCALE_FACTOR=\$(grep 'mapped (' $flagstat | awk '{print 1000000/\$1}')
     echo \$SCALE_FACTOR > ${prefix}.scale_factor.txt
-    genomeCoverageBed -ibam ${bam[0]} -bg -scale \$SCALE_FACTOR $pe_fragment $extend | sort -k1,1 -k2,2n >  ${prefix}.bedGraph
+    genomeCoverageBed -ibam ${bam[0]} -bg -scale \$SCALE_FACTOR $pe_fragment $extend | sort -T '.' -k1,1 -k2,2n >  ${prefix}.bedGraph
 
     bedGraphToBigWig ${prefix}.bedGraph $sizes ${prefix}.bigWig
 
@@ -1213,7 +1213,7 @@ process MergedLibConsensusPeakSet {
     collapsecols = params.narrow_peak ? (["collapse"]*9).join(',') : (["collapse"]*8).join(',')
     expandparam = params.narrow_peak ? "--is_narrow_peak" : ""
     """
-    sort -k1,1 -k2,2n ${peaks.collect{it.toString()}.sort().join(' ')} \\
+    sort -T '.' -k1,1 -k2,2n ${peaks.collect{it.toString()}.sort().join(' ')} \\
         | mergeBed -c $mergecols -o $collapsecols > ${prefix}.txt
 
     macs2_merged_expand.py \\
@@ -1265,7 +1265,7 @@ process MergedLibConsensusPeakSetAnnotate {
         -cpu $task.cpus \\
         > ${prefix}.annotatePeaks.txt
 
-    cut -f2- ${prefix}.annotatePeaks.txt | awk 'NR==1; NR > 1 {print \$0 | "sort -k1,1 -k2,2n"}' | cut -f6- > tmp.txt
+    cut -f2- ${prefix}.annotatePeaks.txt | awk 'NR==1; NR > 1 {print \$0 | "sort -T '.' -k1,1 -k2,2n"}' | cut -f6- > tmp.txt
     paste $bool tmp.txt > ${prefix}.boolean.annotatePeaks.txt
     """
 }
@@ -1517,7 +1517,7 @@ process MergedRepBigWig {
     """
     SCALE_FACTOR=\$(grep 'mapped (' $flagstat | awk '{print 1000000/\$1}')
     echo \$SCALE_FACTOR > ${prefix}.scale_factor.txt
-    genomeCoverageBed -ibam ${bam[0]} -bg -scale \$SCALE_FACTOR $pe_fragment $extend | sort -k1,1 -k2,2n >  ${prefix}.bedGraph
+    genomeCoverageBed -ibam ${bam[0]} -bg -scale \$SCALE_FACTOR $pe_fragment $extend | sort -T '.' -k1,1 -k2,2n >  ${prefix}.bedGraph
 
     bedGraphToBigWig ${prefix}.bedGraph $sizes ${prefix}.bigWig
 
@@ -1680,7 +1680,7 @@ process MergedRepConsensusPeakSet {
     collapsecols = params.narrow_peak ? (["collapse"]*9).join(',') : (["collapse"]*8).join(',')
     expandparam = params.narrow_peak ? "--is_narrow_peak" : ""
     """
-    sort -k1,1 -k2,2n ${peaks.collect{it.toString()}.sort().join(' ')} \\
+    sort -T '.' -k1,1 -k2,2n ${peaks.collect{it.toString()}.sort().join(' ')} \\
         | mergeBed -c $mergecols -o $collapsecols > ${prefix}.txt
 
     macs2_merged_expand.py \\
@@ -1731,7 +1731,7 @@ process MergedRepConsensusPeakSetAnnotate {
         -cpu $task.cpus \\
         > ${prefix}.annotatePeaks.txt
 
-    cut -f2- ${prefix}.annotatePeaks.txt | awk 'NR==1; NR > 1 {print \$0 | "sort -k1,1 -k2,2n"}' | cut -f6- > tmp.txt
+    cut -f2- ${prefix}.annotatePeaks.txt | awk 'NR==1; NR > 1 {print \$0 | "sort -T '.' -k1,1 -k2,2n"}' | cut -f6- > tmp.txt
     paste $bool tmp.txt > ${prefix}.boolean.annotatePeaks.txt
     """
 }