Missing outputfile script added

fischuu · Feb 22, 2021 · a49ad27 · a49ad27
1 parent 2b0d3b3
commit a49ad27
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Showing 3 changed files with 4 additions and 2 deletions.
diff --git a/CHANGELOG b/CHANGELOG
@@ -4,6 +4,7 @@
 #####                                                                      #####
 ################################################################################
 
+0.4.1 : * Bugfix - Missing outputfile script added
 0.4   : Release version
 0.3.16: * Several other small path typos
 0.3.15: * Mixup in samflags anf flagsts solev for final report

diff --git a/GBS-pipeline.smk b/GBS-pipeline.smk
@@ -9,8 +9,8 @@ import os
 ##### Daniel Fischer (daniel.fischer@luke.fi)
 ##### Natural Resources Institute Finland (Luke)
 ##### This pipeline is build upon the the GBS-SNP-CROP pipeline
-##### Version: 0.4
-version = "0.4"
+##### Version: 0.4.1
+version = "0.4.1"
 
 ##### set minimum snakemake version #####
 min_version("5.24")

diff --git a/rules/Module3-MockReference b/rules/Module3-MockReference
@@ -133,6 +133,7 @@ else:
             df -h &> {log}
             echo "Number of threads used:" {threads}
             sed '/^@/d' {input.sam} | cut -f2 | sort | uniq -c > {output.samflags}
+            samtools flagstat {input.sam} > {output.fs}
             samtools stats {input.sam} > {output.stats}
             samtools idxstats {input.sbam} | awk '{{print $1\" \"$3}}' > {output.c}
             bedtools genomecov -ibam {input.sbam} -bg > {output.bed}