同步至HPC-v20190527版

增加Unaligned片段成分分析

tasks/Align.wdl

-task Align {
+task AlignToSenseOnly {
     
-    String sample_ID
+    String sample_id
     File in_fastq
+
+    String refname
+    
     File dir_index
+    String prefix_index 
+
+    Int max_mismatch_allowed
     
-    String prefix_index
+    String docker
+    String cluster_config
+    String disk_size
+
+    command <<<
+        set -o pipefail
+        set -e
+        nt=$(nproc)
 
-    Int sum_unmatch_quality_limit
+        bowtie --threads $nt \
+            ${dir_index}/${prefix_index} --norc \
+            -v ${max_mismatch_allowed} \
+            -q ${in_fastq} \
+            --un ${sample_id}.${refname}Unaligned.fastq \
+            -S ${sample_id}.align2${refname}.sam \
+        2> ${sample_id}.align2${refname}.log
 
+        gzip ${sample_id}.${refname}Unaligned.fastq
+    >>>
+
+    runtime {
+        docker: docker
+        cluster: cluster_config
+        systemDisk: "cloud_ssd 40" 
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        File out_sam="${sample_id}.align2${refname}.sam"
+        File out_fastq="${sample_id}.${refname}Unaligned.fastq.gz"
+        File out_log="${sample_id}.align2${refname}.log"
+    }
+}
+
+task AlignToBothStrand {
+    
+    String sample_id
+    File in_fastq
+
+    String refname
+    
+    File dir_index
+    String prefix_index 
+
+    Int max_mismatch_allowed
+    
     String docker
     String cluster_config
     String disk_size
         set -e
         nt=$(nproc)
 
-
         bowtie --threads $nt \
             ${dir_index}/${prefix_index} \
-            -e ${sum_unmatch_quality_limit} \
+            -v ${max_mismatch_allowed} \
             -q ${in_fastq} \
-            --un ${sample_ID}.matureUnaligned.fastq \
-            -S ${sample_ID}.align2mature.sam \
-        2> ${sample_ID}.align2mature.log
+            --un ${sample_id}.${refname}Unaligned.fastq \
+            -S ${sample_id}.align2${refname}.sam \
+        2> ${sample_id}.align2${refname}.log
+
+        gzip ${sample_id}.${refname}Unaligned.fastq
     >>>
 
     runtime {
         docker: docker
         cluster: cluster_config
-        systemDisk: "cloud_ssd 40"
+        systemDisk: "cloud_ssd 40" 
         dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
     }
 
     output {
-        File out_sam="${sample_ID}.align2mature.sam"
-        File out_fastq="${sample_ID}.matureUnaligned.fastq"
-        File out_log="${sample_ID}.align2mature.log"
+        File out_sam="${sample_id}.align2${refname}.sam"
+        File out_fastq="${sample_id}.${refname}Unaligned.fastq.gz"
+        File out_log="${sample_id}.align2${refname}.log"
     }
-}
+}

tasks/Fastqc.wdl

+task Fastqc {
+	File in_fastq
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		nt=$(nproc)
+		fastqc -t $nt -o ./ ${in_fastq}
+	>>>
+
+	runtime {
+		docker:docker
+        cluster: cluster_config
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File fastqc_html = sub(basename(in_fastq), "\\.(fastq|fq)\\.gz$", "_fastqc.html")
+		File fastqc_zip = sub(basename(in_fastq), "\\.(fastq|fq)\\.gz$", "_fastqc.zip")
+	}
+}

tasks/Quantification.wdl

 task Quantification {
-    String sample_ID
+    String sample_id
     File in_sam
 
     String cluster_config
         set -o pipefail
         set -e
 
-    echo -e "ID.miRNA\tReadCount" > ${sample_ID}.matureMiR.readCount
-    cat ${in_sam} | grep -v '^@'  | awk '($2==0)' | awk '{a[$3]++}END{for(i in a){printf "%s\t%d\n",i,a[i]}}' | sort >> ${sample_ID}.matureMiR.readCount
+    echo -e "ID.miRNA\tReadCount" > ${sample_id}.matureMiR.readCount
+    cat ${in_sam} | grep -v '^@'  | awk '($2==0)' | awk '{a[$3]++}END{for(i in a){printf "%s\t%d\n",i,a[i]}}' | sort >> ${sample_id}.matureMiR.readCount
 
     >>>
 
     }
 
     output {
-        File out_readCount="${sample_ID}.matureMiR.readCount"
+        File out_readCount="${sample_id}.matureMiR.readCount"
     }
 }

tasks/ReadFilter.wdl

 task ReadFilter {
     
-    String sample_ID
+    String sample_id
     File in_fastq
     Int qualified_quality_phred
     Int unqualified_percent_limit
             --n_base_limit ${n_base_limit} \
             --length_required ${length_required} \
             -i ${in_fastq} \
-            -o ${sample_ID}.trimAdapt.filter.fastq.gz \
-            2> ${sample_ID}.filter.log
+            -o ${sample_id}.trimAdapt.filter.fastq.gz \
+            2> ${sample_id}.filter.log
         >>>
 
     runtime {
     }
 
     output {
-        File out_fastq="${sample_ID}.trimAdapt.filter.fastq.gz"
-        File out_log="${sample_ID}.filter.log"
+        File out_fastq="${sample_id}.trimAdapt.filter.fastq.gz"
+        File out_log="${sample_id}.filter.log"
     }
 }

tasks/ReadStats.wdl

 task ReadStats {
     
-    String sample_ID
+    String sample_id
     File in_log_trimAdatper
     File in_log_readFilter
-    File in_log_align_mature
-   
+    File in_log_align_miRNA
+    File in_log_align_preMiRNA
+    File in_log_align_piRNA
+    File in_log_align_tRNA
+    File in_log_align_RNA 
+    File in_log_align_hg38
+    File in_sam_align_RNA
+
     String cluster_config
     String disk_size
 
         set -o pipefail
         set -e
 
-        Total_input=$(cat ${in_log_trimAdatper} | grep 'total reads' | head -n 1 | cut -d ':' -f 2 | sed 's/ //g')
+        n_Total_Sequence=$(cat ${in_log_trimAdatper} | grep 'total reads' | head -n 1 | cut -d ':' -f 2 | sed 's/ //g')
+
+   
 
-        Pass_trimAdatper=$(cat ${in_log_trimAdatper} | grep 'reads passed filter' | tail -n 1  | cut -d ':' -f 2 | sed 's/ //g')
-        Adapter_dimer=$(bc<<<$Total_input-$Pass_trimAdatper)
+        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)
 
-        Too_short=$(cat ${in_log_readFilter} | grep 'too short' | tail -n 1 | cut -d ':' -f 2 | sed 's/ //g')
+        n_Pass_trimAdatper=$(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-$n_Pass_trimAdatper)
+        
+        n_Too_short=$(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_ForAlign=$(cat ${in_log_readFilter} | grep 'reads passed filter' | head -n 1 | cut -d ':' -f 2 | sed 's/ //g')
 
-        Low_quality_singleBase=$(cat ${in_log_readFilter} | grep 'low quality' | head -n 1 | cut -d ':' -f 2 | sed 's/ //g')
-        Low_quality_tooManyN=$(cat ${in_log_readFilter} | grep 'too many N' | head -n 1 | cut -d ':' -f 2 | sed 's/ //g')
-        Low_quality=$(bc<<<$Low_quality_singleBase+$Low_quality_tooManyN)
+        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 ${in_log_align_piRNA} | grep 'at least one reported alignment' | head -n 1 | cut -d ':' -f 2 | cut -d '(' -f 1 | sed 's/ //g')
+        n_tRNA=$(cat ${in_log_align_tRNA} | grep 'at least one reported alignment' | head -n 1 | cut -d ':' -f 2 | cut -d '(' -f 1 | sed 's/ //g')
 
-        ForAlign=$(cat ${in_log_readFilter} | grep 'reads passed filter' | head -n 1 | cut -d ':' -f 2 | sed 's/ //g')
+        n_RNA=$(cat ${in_log_align_RNA} | grep 'at least one reported alignment' | head -n 1 | cut -d ':' -f 2 | cut -d '(' -f 1 | sed 's/ //g')
+        n_otGenomic=$(cat ${in_log_align_hg38} | grep 'at least one reported alignment' | head -n 1 | cut -d ':' -f 2 | cut -d '(' -f 1 | sed 's/ //g')
 
-        Align_miRNA_mature=$(cat ${in_log_align_mature} | grep 'at least one reported alignment' | head -n 1 | cut -d ':' -f 2 | cut -d '(' -f 1 | sed 's/ //g')
+        n_notGenomic=$(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 -e "Stage\tReadCount" > ${sample_ID}.readStats
-        echo -e "Total Input\t$Total_input" >> ${sample_ID}.readStats
-        echo -e "Adapter Dimer\t$Adapter_dimer" >> ${sample_ID}.readStats
-        echo -e "Too Short\t$Too_short" >> ${sample_ID}.readStats
-        echo -e "Low Quality\t$Low_quality" >> ${sample_ID}.readStats
-        echo -e "For Align\t$ForAlign" >> ${sample_ID}.readStats
-        echo -e "Mature miRNA\t$Align_miRNA_mature" >> ${sample_ID}.readStats
-    
+        echo "Pass3"
+        
+       # mkdir -p /cromwell_root/tmp
+        echo "Pass3.1"
+
+        groupedReadCount=/cromwell_root/tmp/${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"
+        
+        file_output=${sample_id}.readStats
+        echo -e "Stage\tReadCount" > $file_output
+        echo -e "adapter not found\t$n_AdapterNotFound" >> $file_output
+        echo -e "adapter dimer\t$n_Adapter_dimer" >> $file_output
+        echo -e "too short\t$n_Too_short" >> $file_output
+        echo -e "low sequencing quality\t$n_Low_quality" >> $file_output
+        echo -e "mature miRNA\t$n_miRNA_mature" >> $file_output
+        echo -e "hairpin miRNA\t$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" >> $file_output
+        echo -e "other from human genome\t$n_otGenomic" >> $file_output
+        echo -e "not from human genome\t$n_notGenomic" >> $file_output
+
+        echo "Pass6"
     >>>
 
     runtime {
     }
 
     output {
-        File out="${sample_ID}.readStats"
+        File out="${sample_id}.readStats"
     }
 }