错误修正

tasks/ReadStats.wdl

@@ -20,22 +20,18 @@ task ReadStats {
 
         n_Total_Sequence=$(cat ${in_log_trimAdatper} | grep 'total reads' | head -n 1 | cut -d ':' -f 2 | sed 's/ //g')
 
-   
-
-        echo "Pass1"
         n_AdapterNotFound=$(cat ${in_log_trimAdatper} | grep 'reads failed due to too long' | cut -d ':' -f 2 | sed 's/ //g')
-        n_Total_forCount=$(bc<<<$n_Total_Sequence-$n_AdapterNotFound)
+        n_Total_forCount=$[$n_Total_Sequence-$n_AdapterNotFound]
 
         n_Pass_trimAdatper=$(cat ${in_log_trimAdatper} | grep 'reads passed filter' | tail -n 1 | cut -d ':' -f 2 | sed 's/ //g')
-        n_Adapter_dimer=$(bc<<<$n_Total_Sequence-$n_AdapterNotFound-$n_Pass_trimAdatper)
+        n_Adapter_dimer=$[$n_Total_Sequence-$n_AdapterNotFound-$n_Pass_trimAdatper]
         
         n_Too_short=$(cat ${in_log_readFilter} | grep 'too short' | tail -n 1 | cut -d ':' -f 2 | sed 's/ //g')
         n_Low_quality_singleBase=$(cat ${in_log_readFilter} | grep 'low quality' | head -n 1 | cut -d ':' -f 2 | sed 's/ //g')
         n_Low_quality_tooManyN=$(cat ${in_log_readFilter} | grep 'too many N' | head -n 1 | cut -d ':' -f 2 | sed 's/ //g')
-        n_Low_quality=$(bc<<<$n_Low_quality_singleBase+$n_Low_quality_tooManyN)
+        n_Low_quality=$[$n_Low_quality_singleBase+$n_Low_quality_tooManyN]
         n_ForAlign=$(cat ${in_log_readFilter} | grep 'reads passed filter' | head -n 1 | cut -d ':' -f 2 | sed 's/ //g')
 
-        echo "Pass2"
         n_miRNA_mature=$(cat ${in_log_align_miRNA} | grep 'at least one reported alignment' | head -n 1 | cut -d ':' -f 2 | cut -d '(' -f 1 | sed 's/ //g')
         n_miRNA_hairpin=$(cat ${in_log_align_preMiRNA} | grep 'at least one reported alignment' | head -n 1 | cut -d ':' -f 2 | cut -d '(' -f 1 | sed 's/ //g')
         n_piRNA=$(cat ${in_log_align_piRNA} | grep 'at least one reported alignment' | head -n 1 | cut -d ':' -f 2 | cut -d '(' -f 1 | sed 's/ //g')
@@ -46,29 +42,47 @@ task ReadStats {
 
         n_notGenomic=$(cat ${in_log_align_hg38} | grep 'reads that failed to align' | head -n 1 | cut -d ':' -f 2 | cut -d '(' -f 1 | sed 's/ //g' )
 
-        echo "Pass3"
-        
-       # mkdir -p /cromwell_root/tmp
-        echo "Pass3.1"
-
-        groupedReadCount=/cromwell_root/tmp/${sample_id}.trimAdapt.filter.align2RNA.grouped.readCount
-        echo "Pass3.2"
-
-       # cat ${in_sam_align_RNA} | head -n 4 
-        echo "Pass3.3"
-
-       # cat ${in_sam_align_RNA} | grep -v '@' | awk '($2!=4)' | cut -f 3 | sed 's/.*;//g' | awk '{a[$1]++}END{for(i in a){printf "%s\t%d\n",i,a[i]}}' > $groupedReadCount
-
-        echo "Pass4"
-
-       # n_mRNA=$(cat $groupedReadCount | grep '^mRNA' | cut -f 2 )
-       # n_lncRNA=$(cat $groupedReadCount | grep '^long_non-coding_RNA' | cut -f 2 )
-       # n_rRNA=$(cat $groupedReadCount | grep '^ribosomal_RNA' | cut -f 2 )
-       # n_YRNA=$(cat $groupedReadCount | grep '^Y_RNA' | cut -f 2 )
-       # n_otsmall=$(cat $groupedReadCount | grep -E '^misc_RNA|small|guide_RNA|vault_RNA' | cut -f 2 | awk '{sum+=$1}END{print sum}')
-       # n_otTranscript=$(bc<<<$n_RNA-$n_mRNA-$n_lncRNA-$n_rRNA-$n_YRNA-$n_otsmall)
-
-        echo "Pass5"
+                
+        groupedReadCount=${sample_id}.trimAdapt.filter.align2RNA.grouped.readCount
+        cat ${in_sam_align_RNA} | grep -v '@' | awk '($2!=4)' | cut -f 3 | sed 's/.*;//g' | awk '{a[$1]++}END{for(i in a){printf "%s\t%d\n",i,a[i]}}' > $groupedReadCount
+
+
+        if [ $(cat $groupedReadCount | grep '^mRNA' | wc -l ) -gt  0]
+        then
+            n_mRNA=$(cat $groupedReadCount | grep '^mRNA' | cut -f 2 )
+        else
+            n_mRNA=0
+        fi
+
+        if [ $(cat $groupedReadCount | grep '^long_non-coding_RNA' | wc -l ) -gt 0 ]
+        then
+            n_lncRNA=$(cat $groupedReadCount | grep '^long_non-coding_RNA' | cut -f 2 )
+        else
+            n_lncRNA=0
+        fi
+
+        if [ $(cat $groupedReadCount | grep '^ribosomal_RNA' | wc -l ) -gt 0 ]
+        then
+            n_rRNA=$(cat $groupedReadCount | grep '^ribosomal_RNA' | cut -f 2 )
+        else
+            n_rRNA=0
+        fi
+
+        if [ $(cat $groupedReadCount | grep '^Y_RNA' | wc -l ) -gt 0 ]
+        then
+            n_YRNA=$(cat $groupedReadCount | grep '^Y_RNA' | cut -f 2 )
+        else
+            n_YRNA=0
+        fi
+
+        if [$(cat $groupedReadCount | grep -E '^misc_RNA|small|guide_RNA|vault_RNA' | wc -l ) -gt 0 ]
+        then
+            n_otsmall=$(cat $groupedReadCount | grep -E '^misc_RNA|small|guide_RNA|vault_RNA' | cut -f 2 | awk '{sum+=$1}END{print sum}')
+        else
+            n_otsmall=0
+        fi
+
+        n_otTranscript=$[$n_RNA-$n_mRNA-$n_lncRNA-$n_rRNA-$n_YRNA-$n_otsmall]
         
         file_output=${sample_id}.readStats
         echo -e "Stage\tReadCount" > $file_output
@@ -80,16 +94,15 @@ task ReadStats {
         echo -e "hairpin miRNA\t$n_miRNA_hairpin" >> $file_output
         echo -e "piRNA\t$n_piRNA" >> $file_output
         echo -e "tRNA\t$n_tRNA" >> $file_output
-       # echo -e "mRNA\t$n_mRNA" >> $file_output
-       # echo -e "lncRNA\t$n_lncRNA" >> $file_output
-       # echo -e "rRNA\t$n_rRNA" >> $file_output
-       # echo -e "YRNA\t$n_YRNA" >> $file_output
-       # echo -e "other small RNA\t$n_otsmall" >> $file_output
-       # echo -e "other from transcriptome\t$n_otTranscript" >> $file_output
+        echo -e "mRNA\t$n_mRNA" >> $file_output
+        echo -e "lncRNA\t$n_lncRNA" >> $file_output
+        echo -e "rRNA\t$n_rRNA" >> $file_output
+        echo -e "YRNA\t$n_YRNA" >> $file_output
+        echo -e "other small RNA\t$n_otsmall" >> $file_output
+        echo -e "other from transcriptome\t$n_otTranscript" >> $file_output
         echo -e "other from human genome\t$n_otGenomic" >> $file_output
         echo -e "not from human genome\t$n_notGenomic" >> $file_output
 
-        echo "Pass6"
     >>>
 
     runtime {
@@ -100,5 +113,6 @@ task ReadStats {
 
     output {
         File out="${sample_id}.readStats"
+        File out_groupedCount="${sample_id}.trimAdapt.filter.align2RNA.grouped.readCount"
     }
 }