Merge pull request #742 from maxplanck-ie/dev_wd

rMats force int when trimmed reads
maxplanck-ie · Jan 18, 2021 · f5c073e · f5c073e
2 parents abee658 + acf491b
commit f5c073e
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/snakePipes/shared/rules/rMats.multipleComp.snakefile b/snakePipes/shared/rules/rMats.multipleComp.snakefile
@@ -64,7 +64,7 @@ rule rMats:
         TMPDIR={params.tempDir}
         MYTEMP=$(mktemp -d ${{TMPDIR:-/tmp}}/snakepipes.XXXXXXXXXX);
         set +o pipefail;
-        readLen=$(samtools view {params.s1} | awk \'{{print length($10)}}\' | head -10000 | awk \'{{ sum += $1 }} END {{ if (NR > 0) print sum / NR }}\')
+        readLen=$(samtools view {params.s1} | awk \'{{print length($10)}}\' | head -10000 | awk \'{{ sum += $1 }} END {{ if (NR > 0) print int(sum / NR) }}\')
         rmats.py --gtf {params.gtf} --b1 {input.b1} --b2 {input.b2} --od {params.od} --tmp $MYTEMP -t {params.end} --libType {params.libType} --readLength $readLen --variable-read-length --nthread {threads} --tstat {threads} 2> {log};
         rm -rf $MYTEMP
 """
diff --git a/snakePipes/shared/rules/rMats.singleComp.snakefile b/snakePipes/shared/rules/rMats.singleComp.snakefile
@@ -44,7 +44,7 @@ rule rMats:
         TMPDIR={params.tempDir}
         MYTEMP=$(mktemp -d ${{TMPDIR:-/tmp}}/snakepipes.XXXXXXXXXX);
         set +o pipefail;
-        readLen=$(samtools view {params.s1} | awk \'{{print length($10)}}\' | head -10000 | awk \'{{ sum += $1 }} END {{ if (NR > 0) print sum / NR }}\')
+        readLen=$(samtools view {params.s1} | awk \'{{print length($10)}}\' | head -10000 | awk \'{{ sum += $1 }} END {{ if (NR > 0) print int(sum / NR) }}\')
         rmats.py --gtf {params.gtf} --b1 {input.b1} --b2 {input.b2} --od {params.od} --tmp $MYTEMP -t {params.end} --libType {params.libType} --readLength $readLen --variable-read-length --nthread {threads} --tstat {threads} 2> {log};
         rm -rf $MYTEMP
 """
diff --git a/snakePipes/shared/rules/rMats.snakefile b/snakePipes/shared/rules/rMats.snakefile
@@ -39,6 +39,6 @@ rule rMats:
     conda: CONDA_RNASEQ_ENV
     shell:"""
         set +o pipefail;
-        readLen=$(samtools view {params.s1} | awk \'{{print length($10)}}\' | head -10000 | awk \'{{ sum += $1 }} END {{ if (NR > 0) print sum / NR }}\')
+        readLen=$(samtools view {params.s1} | awk \'{{print length($10)}}\' | head -10000 | awk \'{{ sum += $1 }} END {{ if (NR > 0) print int(sum / NR) }}\')
         rmats.py --gtf {params.gtf} --b1 {input.b1} --b2 {input.b2} --od {params.od} --tmp {params.tempDir} -t {params.end} --libType {params.libType} --readLength $readLen --variable-read-length --nthread {threads} --tstat {threads} 2> {log}
 """