PAS-seq nf and config : fix beugs

src/PASseq.config

@@ -33,45 +33,16 @@ profiles {
         queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
         penv = 'openmp16'
       }
-      withName: sort_bam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/samtools_1.7"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "20GB"
-        time = "12h"
-        queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
-      }
-      withName: index_bam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/samtools_1.7"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "20GB"
-        time = "12h"
-        queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
-      }
-      withName: dedup {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "umi_tools/1.0.0"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "20GB"
-        time = "12h"
-        queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
-      }
-      withName: counting {
+      withName: bam_to_bigwig {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "htseq/0.11.2"
+        module = "deeptools/3.0.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "20GB"
-        time = "12h"
-        queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
       }
     }
   }
@@ -91,17 +62,13 @@ profiles {
         cpus = 4
         container = "lbmc/hisat2:2.1.0"
       }
-      withName: sort_bam {
-        container = "lbmc/samtools:1.7"
-        cpus = 1
-      }
       withName: index_bam {
         container = "lbmc/samtools:1.7"
-        cpus = 1
+        cpus = 4
       }
-      withName: dedup {
-        container = "lbmc/umi_tools:1.0.0"
-        cpus = 1
+      withName: bam_to_bigwig {
+        container = "lbmc/deeptools:3.0.2"
+        cpus = 4
       }
       withName: counting {
         container = "lbmc/htseq:0.11.2"

src/PASseq.nf

@@ -55,8 +55,14 @@ process rRNA_removal {
   file "*.txt" into bowtie_report
 
   script:
+  index_id = index[0]
+  for (index_file in index) {
+    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
+        index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
+    }
+  }
 """
-zcat ${reads} | bowtie2 --sensitive -p ${task.cpus} -x human_rRNA_tRNA \
+zcat ${reads} | bowtie2 --sensitive -p ${task.cpus} -x ${index_id} \
 -U - --un-gz ${file_id}_mRNA.fastq.gz 2> \
 ${file_id}_bowtie2_report.txt > /dev/null
 
@@ -92,11 +98,17 @@ process hisat2_human {
     file "*.txt" into hisat_report
 
   script:
+  index_id = index[0]
+  for (index_file in index) {
+    if (index_file =~ /.*\.1\.ht2/ && !(index_file =~ /.*\.rev\.1\.ht2/)) {
+        index_id = ( index_file =~ /(.*)\.1\.ht2/)[0][1]
+    }
+  }
 """
-hisat2 -x genome_tran -p ${task.cpus} \
--U ${fastq_filtred} --un-gz ${file_id}_notaligned_hg38.fastq.gz \
+hisat2 -x ${index_id} -p ${task.cpus} \
+-U ${fastq_filtred} --un-gz ${file_id}_notaligned.fastq.gz \
 --end-to-end  --rna-strandness 'F' \
-2> ${file_id}_hisat2_hg38.txt | samtools view -bS -F 4 -o ${file_id}.bam
+2> ${file_id}_hisat2.txt | samtools view -bS -F 4 -o ${file_id}.bam
 
 """
 }
@@ -105,64 +117,25 @@ hisat2 -x genome_tran -p ${task.cpus} \
 
 process index_bam {
   tag "$file_id"
-  publishDir "${params.output}/03_hisat2_hg38/", mode: 'copy'
+  publishDir "${params.output}/03_mapping/", mode: 'copy'
 
   input:
     set file_id, file(bam) from reads_aligned_hg38
+    file report from hisat_report
 
   output:
     set file_id, "*_sorted.{bam,bam.bai}" into sorted_bam_files
+    file "*.log" into hisat_report_bis
 
   script:
 """
 samtools sort -@ ${task.cpus} -O BAM -o ${file_id}_sorted.bam ${bam}
 samtools index ${file_id}_sorted.bam
+cat ${report} > ${file_id}.log
 """
 }
 
-sorted_bam_files.into{for_dedup;for_htseq}
-
-/*                   deduplicating reads                            */
-
-params.dedup_options = ""
-
-process dedup {
-  tag "$file_id"
-
-  input:
-  set file_id, file(bam) from for_dedup
-
-  output:
-  set file_id, "*dedup.bam" into dedup_bam
-  file "*.txt" into dedup_report
-
-  script:
-"""
-umi_tools dedup -I ${bam[0]} \
-                ${params.dedup_options} \
-                -S ${file_id}_dedup.bam > report.txt
-"""
-}
-
-process sort_bam {
-  tag "$file_id"
-  publishDir "${params.output}/03_hisat2_hg38_dedup/", mode: 'copy'
-
-  input:
-    set file_id, file(bam) from dedup_bam
-    file dedup from dedup_report
-
-  output:
-    set file_id, "*_sorted.{bam,bam.bai}" into sorted_bam_files_2
-    file "*.txt" into report_dedup
-
-  script:
-"""
-samtools sort -@ ${task.cpus} -O BAM -o ${file_id}_sorted.bam ${bam}
-samtools index ${file_id}_sorted.bam
-cat ${dedup} > ${file_id}_dedup_report.txt
-"""
-}
+sorted_bam_files.into{for_htseq}
 
 /*                   HTseq                            */
 
@@ -188,22 +161,11 @@ process counting {
   script:
 """
 htseq-count ${bam[0]} ${gtf} \
-            --mode=intersection-nonempty \
-            -a 10 \
-            -s yes \
-            -t CDS \
-            -i gene_id \
-            -r pos \
-            -f bam \
-> ${file_id}_CDS.count
-
-htseq-count ${bam[0]} ${gtf} \
-            --mode=intersection-nonempty \
+            --mode=union \
             -a 10 \
             -s yes \
             -t exon \
             -i gene_id \
-            -r pos \
             -f bam \
 > ${file_id}_exon.count