......

tasks/samtools.wdl

@@ -14,9 +14,9 @@ task samtools {
        set -o pipefail
        set -e
        /opt/conda/bin/samtools view -bS ${sam} > ${bam}
-       /opt/conda/bin/samtools view -bs 42.1 ${bam} > ${percent_bam}
        /opt/conda/bin/samtools sort -m 1000000000 ${bam} -o ${sorted_bam}
        /opt/conda/bin/samtools index ${sorted_bam}
+       /opt/conda/bin/samtools view -bs 42.1 ${sorted_bam} > ${percent_bam}
        /opt/conda/bin/samtools stats -i ${insert_size} ${sorted_bam} |grep ^IS|cut -f 2- > ${sample_id}.ins_size
     >>>
 

tasks/stringtie.wdl

@@ -12,7 +12,7 @@ task stringtie {
     command <<<
       nt=$(nproc)
       mkdir ballgown
-      /opt/conda/bin/stringtie -e -B -p $nt -f ${minimum_isoform_abundance} -m ${minimum_length_allowed_for_the_predicted_transcripts} -a ${Junctions_no_spliced_reads} -M ${maximum_fraction_of_muliplelocationmapped_reads} -G ${gtf} -o ballgown/${sample_id}/${sample_id}.gtf -C ${sample_id}.cov.ref.gtf -A ${sample_id}.gene.abundance.txt ${bam} -g ${sample_id}_genecount.csv
+      /opt/conda/bin/stringtie -e -B -p $nt -f ${minimum_isoform_abundance} -m ${minimum_length_allowed_for_the_predicted_transcripts} -a ${Junctions_no_spliced_reads} -M ${maximum_fraction_of_muliplelocationmapped_reads} -G ${gtf} -o ballgown/${sample_id}/${sample_id}.gtf -C ${sample_id}.cov.ref.gtf -A ${sample_id}.gene.abundance.txt ${bam}
     >>>
     
     runtime {

workflow.wdl

@@ -78,7 +78,7 @@ workflow {{ project_name }} {
 		docker = fastp_docker,
 		cluster = fastp_cluster,
 		adapter_sequence = adapter_sequence,
-    	adapter_sequence_r2 = adapter_sequence_r2,
+		adapter_sequence_r2 = adapter_sequence_r2,
 		umi_loc = umi_loc,
 		trim_front1 = trim_front1,
 		trim_tail1 = trim_tail1, 
@@ -137,12 +137,12 @@ workflow {{ project_name }} {
 		input: 
 		sample_id = quartet[2],
 		sam = hisat2.sam,
-        docker = samtools_docker,
+		docker = samtools_docker,
 		cluster = samtools_cluster,
 		insert_size = insert_size
 		}
-        
-        call qualimapBAMqc.qualimapBAMqc as qualimapBAMqc {
+				
+		call qualimapBAMqc.qualimapBAMqc as qualimapBAMqc {
 		input:
 		bam = samtools.out_percent,
 		docker = qualimapBAMqc_docker,
@@ -167,9 +167,9 @@ workflow {{ project_name }} {
 		docker = stringtie_docker,
 		cluster = stringtie_cluster,
 		minimum_length_allowed_for_the_predicted_transcripts = minimum_length_allowed_for_the_predicted_transcripts,
-    	Junctions_no_spliced_reads = Junctions_no_spliced_reads,
-    	minimum_isoform_abundance = minimum_isoform_abundance,
-    	maximum_fraction_of_muliplelocationmapped_reads = maximum_fraction_of_muliplelocationmapped_reads
+		Junctions_no_spliced_reads = Junctions_no_spliced_reads,
+		minimum_isoform_abundance = minimum_isoform_abundance,
+		maximum_fraction_of_muliplelocationmapped_reads = maximum_fraction_of_muliplelocationmapped_reads
 		}
 	}