Bugfix

paulsengroup · Feb 9, 2024 · 71d9f49 · 71d9f49
1 parent df956e1
commit 71d9f49
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Showing 2 changed files with 21 additions and 3 deletions.
diff --git a/benchmarks/workflows/benchmark_load.nf b/benchmarks/workflows/benchmark_load.nf
@@ -86,9 +86,18 @@ process preprocess_pairs_zst {
         '''
         set -o pipefail
 
+        cat > header.txt <<- EOM
+        ## pairs format v1.0
+        #sorted: chr1-chr2-pos1-pos2
+        #shape: upper triangle
+        #columns: readID chr1 pos1 chr2 pos2 strand1 strand2
+        EOM
+
+        cat header.txt | zstd -19 > '!{outname}'
+
         zcat '!{pairs}' |
         grep -P 'chr[\\dXY]+\\s\\d+\\schr[\\dXY]+\\s' |
-        zstd -T'!{task.cpus}' -19 -o '!{outname}'
+        zstd -T'!{task.cpus}' -19 >> '!{outname}'
         '''
 }
 
@@ -106,9 +115,18 @@ process preprocess_pairs_gz {
         '''
         set -o pipefail
 
+        cat > header.txt <<- EOM
+        ## pairs format v1.0
+        #sorted: chr1-chr2-pos1-pos2
+        #shape: upper triangle
+        #columns: readID chr1 pos1 chr2 pos2 strand1 strand2
+        EOM
+
+        cat header.txt | pigz -9 > '!{outname}'
+
         zcat '!{pairs}' |
         grep -P 'chr[\\dXY]+\\s\\d+\\schr[\\dXY]+\\s' |
-        pigz -p '!{task.cpus}' -9 > '!{outname}'
+        pigz -p '!{task.cpus}' -9 >> '!{outname}'
         '''
 }
 

diff --git a/bin/run_hic_tools_pre.sh b/bin/run_hic_tools_pre.sh
@@ -12,7 +12,7 @@ fi
 
 path_to_pairs="$1"
 path_to_output="$2"
-tmpdir="$(mktemp -d -t "$3/hictk-tmp-XXXXXXXXXX")"
+tmpdir="$(mktemp -d -p "$3" -t "hictk-tmp-XXXXXXXXXX")"
 hic_tools_jar="$4"
 resolution="$5"
 cpus="$6"