Pass --no-name to gzip whenever possible

oist · Oct 9, 2024 · 264035e · 264035e
1 parent 2897974
commit 264035e
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/modules/local/mergemasks.nf b/modules/local/mergemasks.nf
@@ -27,10 +27,10 @@ process MERGE_MASKS {
     bedtools jaccard -nonamecheck -a $tantan       -b $repeatmasker         > ${prefix}_tantan_repeatmasker_jaccard.txt
     bedtools jaccard -nonamecheck -a $repeatmasker -b $windowmasker         > ${prefix}_repeatmasker_windowmasker_jaccard.txt
 
-    zcat $tantan $windowmasker               | sort -k1,1 -k2,2n | bedtools merge | gzip --best  > ${prefix}_tantan_windowmasker.bed.gz
-    zcat $tantan $repeatmasker               | sort -k1,1 -k2,2n | bedtools merge | gzip --best  > ${prefix}_tantan_repeatmasker.bed.gz
-    zcat $windowmasker $repeatmasker         | sort -k1,1 -k2,2n | bedtools merge | gzip --best  > ${prefix}_windowmasker_repeatmasker.bed.gz
-    zcat $tantan $windowmasker $repeatmasker | sort -k1,1 -k2,2n | bedtools merge | gzip --best  > ${prefix}_allmaskers.bed.gz
+    zcat $tantan $windowmasker               | sort -k1,1 -k2,2n | bedtools merge | gzip --best --no-name > ${prefix}_tantan_windowmasker.bed.gz
+    zcat $tantan $repeatmasker               | sort -k1,1 -k2,2n | bedtools merge | gzip --best --no-name > ${prefix}_tantan_repeatmasker.bed.gz
+    zcat $windowmasker $repeatmasker         | sort -k1,1 -k2,2n | bedtools merge | gzip --best --no-name > ${prefix}_windowmasker_repeatmasker.bed.gz
+    zcat $tantan $windowmasker $repeatmasker | sort -k1,1 -k2,2n | bedtools merge | gzip --best --no-name > ${prefix}_allmaskers.bed.gz
 
     bedtools \\
         maskfasta \\

diff --git a/modules/local/seqtk.nf b/modules/local/seqtk.nf
@@ -25,7 +25,7 @@ process SEQTK_CUTN {
     # Produces a compressed BED-3 file with the coordinates of soft-masked regions.
     zcat -f $fasta | awk '/^>/ {print; next} {gsub(/[acgt]/, "N"); print}' |
         seqtk cutN -gn 1 -p 100000 - |
-        gzip --best > ${prefix}.mask.bed.gz
+        gzip --best --no-name > ${prefix}.mask.bed.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -38,7 +38,7 @@ process SEQTK_CUTN {
 
     """
     touch ${prefix}.mask.bed
-    gzip --best ${prefix}.mask.bed
+    gzip --best --no-name ${prefix}.mask.bed
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":