revise samtools sort -m

defaults

@@ -33,9 +33,9 @@
     "stringtie_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/stringtie:v1.3.4",
     "stringtie_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
     "ballgown_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/pgx-ballgown:0.0.1",
-    "ballgown_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
+    "ballgown_cluster": "OnDemand bcs.ps.g.large img-ubuntu-vpc",
     "count_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/count:v1.0",
-    "count_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
+    "count_cluster": "OnDemand bcs.ps.g.large img-ubuntu-vpc",
     "insert_size":"8000",
     "count_length": "150"
 }

tasks/fastp.wdl

@@ -26,7 +26,7 @@ task fastp {
     ## Trim
     if [ "${trim_adapter}" != 'true' ]; then
     cp ${read1} ${sample_id}_R1.fq.gz
-	cp ${read2} ${sample_id}_R2.fq.gz
+    cp ${read2} ${sample_id}_R2.fq.gz
     else
     fastp --thread $nt -l ${length_required} -q ${qualified_quality_phred} -u ${length_required1} --adapter_sequence ${adapter_sequence} --adapter_sequence_r2 ${adapter_sequence_r2} --detect_adapter_for_pe --trim_front1 ${trim_front1} --trim_tail1 ${trim_tail1} --max_len1 ${max_len1} --trim_front2 ${trim_front2} --trim_tail2 ${trim_tail2} --max_len2 ${max_len2} -i ${read1} -I ${read2} -o ${sample_id}_R1.fq.gz -O ${sample_id}_R2.fq.gz -j ${sample_id}.json -h ${sample_id}.html
     fi

tasks/samtools.wdl

@@ -17,9 +17,9 @@ task samtools {
        nt=$(nproc)
        /opt/conda/bin/samtools view -@ $nt -bS ${sam} > ${bam}
        /opt/conda/bin/samtools sort -@ $nt -m 1000000000 ${bam} -o ${sorted_bam}
-       /opt/conda/bin/samtools index -@ $nt ${sorted_bam}
-       /opt/conda/bin/samtools stats -@ $nt ${sorted_bam} > ${samstats}
-       /opt/conda/bin/samtools stats -@ $nt -i ${insert_size} ${sorted_bam} |grep ^IS|cut -f 2- > ${ins_size}
+       /opt/conda/bin/samtools index ${sorted_bam}
+       /opt/conda/bin/samtools stats ${sorted_bam} > ${samstats}
+       /opt/conda/bin/samtools stats -i ${insert_size} ${sorted_bam} |grep ^IS|cut -f 2- > ${ins_size}
     >>>
 
     runtime {