revise samtools output

tasks/count.wdl

     }
     
     output {
-      File mat_expression_genecount = "${sample_id}_gene_count_matrix.csv"
-      File mat_expression_transcriptcount = "${sample_id}_transcript_count_matrix.csv"
+      File mat_expression_genecount="${sample_id}_gene_count_matrix.csv"
+      File mat_expression_transcriptcount="${sample_id}_transcript_count_matrix.csv"
     }
 }

tasks/fastqscreen.wdl

 	File read2
 	File screen_ref_dir
 	File fastq_screen_conf
-	String read1name = sub(basename(read1),"\\.\\S+$", "")
-	String read2name = sub(basename(read2),"\\.\\S+$", "")
+	String read1name=sub(basename(read1),"\\.\\S+$", "")
+	String read2name=sub(basename(read2),"\\.\\S+$", "")
 	String docker
 	String cluster
 	String disk_size

tasks/hisat2.wdl

    File read_1P
    File read_2P
    String idx_prefix
-   String base = sub(basename(read_1P),"\\.\\S+$", "")
+   String base=sub(basename(read_1P),"\\.\\S+$", "")
    String docker
    String cluster
    String disk_size

tasks/qualimap.wdl

 	File bam
 	File bai
 	File gtf
-	String bamname = basename(bam, ".sorted.bam")
+	String bamname=basename(bam, ".sorted.bam")
 	String docker
 	String cluster
 	String disk_size
 	}
 
 	output {
-		File bamqc_gz = "${bamname}_bamqc_qualimap.tar.gz"
-		File rnaseq_gz = "${bamname}_rnaseq_qualimap.tar.gz"
+		File bamqc_gz="${bamname}_bamqc_qualimap.tar.gz"
+		File rnaseq_gz="${bamname}_rnaseq_qualimap.tar.gz"
 	}
 }

tasks/samtools.wdl

 task samtools {
     File sam
-    String base = basename(sam, ".sam")
-    String bam = base + ".bam"
-    String sorted_bam = base + ".sorted.bam"
-    String sorted_bam_index = base + ".sorted.bam.bai"
-    String viral_samstats = base + ".viral.samstats"
+    String base=basename(sam, ".sam")
+    String bam=base + ".bam"
+    String out_unsort_bam=base + ".bam"
+    String out_sort_bam=base + ".sorted.bam"
+    String out_sort_bam_index=base + ".sorted.bam.bai"
+    String samstats=base + ".samstats"
     String docker
     String cluster
     String disk_size
        /opt/conda/bin/samtools view -bS ${sam} > ${bam}
        /opt/conda/bin/samtools sort -m 1000000000 ${bam} -o ${sorted_bam}
        /opt/conda/bin/samtools index ${sorted_bam}
-       /opt/conda/bin/samtools stats ${sorted_bam} > ${viral_samstats}
+       /opt/conda/bin/samtools stats ${sorted_bam} > ${samstats}
     >>>
 
     runtime {
     }
 
     output {
-      File out_bam = sorted_bam
-      File out_bam_index = sorted_bam_index
-      File out_viral_samstats = viral_samstats
+      File out_unsort_bam=bam
+      File out_sort_bam=sorted_bam
+      File out_sort_bam_index=sorted_bam_index
+      File out_samstats=samstats
     }
 
 }

tasks/stringtie.wdl

     File bam
     File gtf
     String docker
-    String base = basename(bam, ".sorted.bam")
+    String base=basename(bam, ".sorted.bam")
     String cluster
     String disk_size
 
     }
     
     output {
-      File covered_transcripts = "${base}.cov.ref.gtf"
-      File gene_abundance = "${base}.gene.abundance.txt"
-      Array[File] ballgown = ["ballgown/${base}/${base}.gtf", "ballgown/${base}/e2t.ctab", "ballgown/${base}/e_data.ctab", "ballgown/${base}/i2t.ctab", "ballgown/${base}/i_data.ctab", "ballgown/${base}/t_data.ctab"]
+      File covered_transcripts="${base}.cov.ref.gtf"
+      File gene_abundance="${base}.gene.abundance.txt"
+      Array[File] ballgown=["ballgown/${base}/${base}.gtf", "ballgown/${base}/e2t.ctab", "ballgown/${base}/e_data.ctab", "ballgown/${base}/i2t.ctab", "ballgown/${base}/i_data.ctab", "ballgown/${base}/t_data.ctab"]
     }
 }

workflow.wdl

 
 	call qualimap.qualimap as qualimap {
 		input:
-		bam=samtools.out_bam,
-		bai=samtools.out_bam_index,
+		bam=samtools.out_unsort_bam,
 		gtf=gtf, 
 		docker=qualimap_docker,
 		cluster=qualimap_cluster,
 		docker=stringtie_docker,
 		cluster=stringtie_cluster,
 		gtf=gtf, 
-		bam=samtools.out_bam,
+		bam=samtools.out_sort_bam,
 		disk_size=disk_size
 		}