modify RNAseq script and adapt queue for lake

src/RNAseq.config

@@ -9,49 +9,46 @@ profiles {
         cpus = 1
         memory = "20GB"
         time = "12h"
-        queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+        queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: rRNA_removal {
         beforeScript = "source $baseDir/.conda_psmn.sh"
         conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
-        cpus = 16
-        memory = "30GB"
-        time = "24h"
-        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
-        penv = 'openmp16'
+	queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+	penv = 'openmp32'
       }
       withName: hisat2_human {
         beforeScript = "source $baseDir/.conda_psmn.sh"
-        module = "$baseDir/.conda_envs/hisat2_2.1.0"
+        conda = "$baseDir/.conda_envs/hisat2_2.1.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         memory = "20GB"
         cpus = 16
         time = "12h"
-        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
-        penv = 'openmp16'
+        queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+        penv = 'openmp32'
       }
       withName: sort_bam {
         beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/samtools_1.7"
+        conda = "$baseDir/.conda_envs/hisat2_2.1.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
         memory = "20GB"
         time = "12h"
-        queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+        queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: index_bam {
         beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/samtools_1.7"
+        conda = "$baseDir/.conda_envs/hisat2_2.1.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
         memory = "20GB"
         time = "12h"
-        queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+        queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: dedup {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -61,7 +58,7 @@ profiles {
         cpus = 1
         memory = "20GB"
         time = "12h"
-        queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+        queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: counting {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -71,7 +68,7 @@ profiles {
         cpus = 1
         memory = "20GB"
         time = "12h"
-        queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+        queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
     }
   }

src/RNAseq.nf

@@ -27,6 +27,7 @@ process trimming {
   script:
   """
   cutadapt -a AGATCGGAAGAGC -A AGATCGGAAGAGC \
+  --minimum-length 50 \
   -o ${file_id}_cut_R1.fastq.gz -p ${file_id}_tmp_R2.fastq.gz \
   ${reads[0]} ${reads[1]} > ${file_id}_report.txt
 
@@ -50,7 +51,7 @@ Channel
 process rRNA_removal {
   tag "$file_id"
   cpus 8
-  publishDir "results/RNAseq/U937/02_rRNA_depletion/", mode: 'copy'
+  publishDir "results/RNAseq/02_rRNA_depletion/", mode: 'copy'
 
   input:
   set file_id, file(reads) from fastq_files_cut
@@ -107,26 +108,31 @@ hisat2 -x genome_tran -p ${task.cpus} \
 """
 }
 
+reads_aligned_hg38.into{for_mapping;for_htseq}
+
+
 /*                   sorting                             */
 
 process index_bam {
   tag "$file_id"
-  publishDir "${params.output}/03_hisat2_hg38/", mode: 'copy'
+  publishDir "results/RNAseq/03_hisat2_hg38/", mode: 'copy'
 
   input:
-    set file_id, file(bam) from reads_aligned_hg38
+    set file_id, file(bam) from for_mapping 
+    file report from hisat_report
 
   output:
     set file_id, "*_sorted.{bam,bam.bai}" into sorted_bam_files
+    file "*.txt" into report_hisat
 
   script:
 """
 samtools sort -@ ${task.cpus} -O BAM -o ${file_id}_sorted.bam ${bam}
 samtools index ${file_id}_sorted.bam
+cat ${report} > ${file_id}_hisat_hg38.txt
 """
 }
 
-sorted_bam_files.into{for_dedup;for_htseq}
 
 /*                   deduplicating reads
 
@@ -172,6 +178,21 @@ cat ${dedup} > ${file_id}_dedup_report.txt
 
 /*                   HTseq                            */
 
+process sort_bam {
+  tag "$file_id"
+
+  input:
+    set file_id, file(bam) from for_htseq
+
+  output:
+    set file_id, "*_sorted.bam" into sorted_bam_files_2
+
+  script:
+"""
+samtools sort -@ ${task.cpus} -n -O BAM -o ${file_id}_sorted.bam ${bam}
+"""
+} 
+
 params.gtf = "$baseDir/data/annotation/*.gtf"
 log.info "gtf files : ${params.gtf}"
 
@@ -182,10 +203,10 @@ Channel
 
 process counting {
   tag "$file_id"
-  publishDir "${params.output}/04_HTseq/", mode: 'copy'
+  publishDir "results/RNAseq/04_HTseq/", mode: 'copy'
 
   input:
-  set file_id, file(bam) from for_htseq
+  set file_id, file(bam) from sorted_bam_files_2
   file gtf from gtf_file.toList()
 
   output:
@@ -199,7 +220,6 @@ htseq-count ${bam[0]} ${gtf} \
             -s yes \
             -t CDS \
             -i gene_id \
-            -r pos \
             -f bam \
 > ${file_id}_CDS.count
 
@@ -209,7 +229,6 @@ htseq-count ${bam[0]} ${gtf} \
             -s yes \
             -t exon \
             -i gene_id \
-            -r pos \
             -f bam \
 > ${file_id}_exon.count