rename log file

fei0810 · Apr 7, 2021 · b718b01 · b718b01
1 parent 927cb40
commit b718b01
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Showing 3 changed files with 13 additions and 8 deletions.
diff --git a/tritimap/rules/denovo_sacffold_filter_by_fasta.smk b/tritimap/rules/denovo_sacffold_filter_by_fasta.smk
@@ -19,7 +19,7 @@ rule uniqScaffoldByFasta:
     message: "\nGet bulk uniq scaffolds by fasta file. Input file: {input.fa}\n"
     threads: thread
     log:
-        join(dir_path+"/logs", "_".join(samples.bulk.drop_duplicates()) + "_uniqscaffold.log")
+        join(dir_path+"/logs", "_".join(samples.bulk.drop_duplicates()) + "_uniqscaffold_byfasta.log")
     shell:"""
     set +e
     bash {params.scriptdir}/getuniqscaffold_by_fasta.sh {input.fa} {params.database} {params.length} {params.genome} {threads} {params.datatype} {params.memory} {output.scaffold1} {output.scaffold2} {output.unmap1} {output.unmap2} > {log} 2>&1

diff --git a/tritimap/rules/denovo_scaffold_filter_by_region.smk b/tritimap/rules/denovo_scaffold_filter_by_region.smk
@@ -19,7 +19,7 @@ rule uniqScaffoldByRegion:
     message: "\nGet uniq scaffolds by region file. Input file: {input.fa}\n"
     threads: thread
     log:
-        join(dir_path+"/logs", "_".join(samples.bulk.drop_duplicates()) + "_uniqscaffold.log")
+        join(dir_path+"/logs", "_".join(samples.bulk.drop_duplicates()) + "_uniqscaffold_byregion.log")
     shell:"""
     set +e
     cat {input.region} | tr ',' '\t' | awk '{{print $1"\tqtl\t"$2"\t"$3}}' > {output.region}

diff --git a/tritimap/rules/dna_mapping.smk b/tritimap/rules/dna_mapping.smk
@@ -13,15 +13,20 @@ rule dnaBWAmem2Mapping:
         errormap = dir_path+"/03_mappingout/{bulk}_{bulktype}.errormap.sort.bam",
         unmap = dir_path+"/03_mappingout/{bulk}_{bulktype}.unmap.bam"
     threads: thread
+    log:
+        dir_path+"/logs/{bulk}_{bulktype}_bwamem2.log"
     message: "Mapping {input} with BWA-mem2"
     run:
         shell("""
         bwa-mem2 mem -v 1 -t {threads} -M -Y -R '{params.group}' {params.genome} {input} | \
-        samtools sort -@ {threads} -o {output.raw} - ;
-        samtools view -h -f 3 {output.raw} | egrep -v 'XA:Z|SA:Z' | samtools sort -@ {threads} -o {output.truemap} ;
-        samtools view -h {output.raw} | egrep '^@|XA:Z|SA:Z' | samtools sort -@ {threads} -o {output.errormap} ;
+        samtools sort -@ {threads} -o {output.raw} -;
+        echo "raw.down" ;
+        samtools view -h -f 3 {output.raw} | egrep -v 'XA:Z|SA:Z' | samtools sort -@ {threads} -o {output.truemap} -;
+        echo "true.down" ;
+        samtools view -h {output.raw} | egrep '^@|XA:Z|SA:Z' | samtools sort -@ {threads} -o {output.errormap} -;
+        echo "error.down" ;
         samtools view -f 4 -b {output.raw} > {output.unmap} ;
-        samtools index -c {output.raw};
-        samtools index -c {output.truemap};
-        samtools index -c {output.errormap};
+        samtools index -c {output.raw} ;
+        samtools index -c {output.truemap} ;
+        samtools index -c {output.errormap}
     """)