Reditools3

config/ressources/hpc.config

@@ -32,4 +32,8 @@ process {
         cpus = 6
         time = '4d'
     }
+    withName: 'bamutil' {
+	cpus = 8
+	memory = '48G'
+    }
 }

config/softwares.config

@@ -10,7 +10,7 @@ process {
     }
     withLabel: 'bowtie2' {
         container = 'quay.io/biocontainers/bowtie2:2.5.1--py38he00c5e5_2'
-  	}
+    }
     withLabel: 'bwa' {
         container = 'quay.io/biocontainers/bwa:0.7.3a--he4a0461_9'
     }
@@ -24,20 +24,20 @@ process {
         container = 'quay.io/biocontainers/hisat2:2.2.1--hdbdd923_6'
     }
     withLabel: "jacusa2" {
-        container = singularity.enabled ? "${sifPath}/jacusa2.sif" : "jacusa2"
+        container = singularity.enabled ? "${params.sifPath}/jacusa2.sif" : "jacusa2"
         containerOptions = '--ulimit nofile=1024:1024'    // Limit number of file descriptors to avoid out of memory errors
     }
     withLabel: 'minimap2' {
         container = 'quay.io/biocontainers/minimap2:2.26--he4a0461_1'
     }
     withLabel: 'pigz' {
         container = 'quay.io/biocontainers/pigz:2.8'
-  	}
+    }
     withLabel: "reditools2" {
-        container = singularity.enabled ? "${sifPath}/reditools2.sif" : "reditools2"
+        container = singularity.enabled ? "${params.sifPath}/reditools2.sif" : "reditools2"
     }
     withLabel: "reditools3" {
-        container = singularity.enabled ? "${sifPath}/reditools3.sif" : "reditools3"
+        container = singularity.enabled ? "${params.sifPath}/reditools3.sif" : "reditools3"
     }
     withLabel: 'rsem' {
         container = 'quay.io/biocontainers/rsem:1.3.3--pl5321h0033a41_7'
@@ -49,12 +49,12 @@ process {
         container = 'quay.io/biocontainers/samtools:1.3.1--h0cf4675_11'
     }
     withLabel: "sapin" {
-        container = singularity.enabled ? "${sifPath}/sapin.sif" : "sapin"
+        container = singularity.enabled ? "${params.sifPath}/sapin.sif" : "sapin"
     }
     withLabel: 'multiqc' {
         container = 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0'
     }
     withLabel: "pluviometer" {
-        container = singularity.enabled ? "${sifPath}/pluviometer.sif" : "pluviometer"
+        container = singularity.enabled ? "${params.sifPath}/pluviometer.sif" : "pluviometer"
     }
 }

modules/bamutil.nf

@@ -13,7 +13,7 @@ process bamutil_clipoverlap {
     script:
 
         """
-        bam clipOverlap --storeOrig CG --poolSize 5000000 --in ${bam} --out ${bam}_clipoverlap.bam --stats > ${meta.id}_bamutil_clipoverlap.log
+        bam clipOverlap --storeOrig CG --poolSize 5000000 --in ${bam} --out ${bam}_clipoverlap.bam --stats --excludeFlags 0x37 > ${meta.id}_bamutil_clipoverlap.log
         """
 
 }

modules/reditools3.nf

@@ -31,6 +31,6 @@ process reditools3 {
         base_name = bam.BaseName
 
         """
-        python -m reditools analyze ${bam} --reference ${genome} --strand ${strand_orientation} --output-file ${base_name}.site_edits_reditools3.txt --threads ${task.cpus} --verbose > ${base_name}.reditools3.log
+        python -m reditools analyze ${bam} --reference ${genome} --strand ${strand_orientation} --output-file ${base_name}.site_edits_reditools3.txt --threads ${task.cpus} --verbose &> ${base_name}.reditools3.log
         """
 }

nextflow.config

@@ -21,18 +21,18 @@ includeConfig "$baseDir/config/ressources/base.config"
 profiles {
 
     itrop {
-        executor {
-            name = 'slurm'
-        }
         process {
-            scratch = '/scratch-ib'
-            clusterOptions = "--constraint=infiniband"
+	   executor = 'slurm'
+	   queue = 'normal'  
+           scratch = '/scratch-ib'
+           clusterOptions = "--constraint=infiniband"
         }
+
         singularity.enabled = true
-        // singularity.envWhitelist = '' // Comma separated list of environment variable names to be included in the container environment.
+        params.sifPath = "${baseDir}/sif_images"
+        // singularity.envWhitelist = '' // Comma separated list of environment variable names to be included in the container environment.	
         includeConfig "$baseDir/config/softwares.config"
         includeConfig "$baseDir/config/ressources/hpc.config"
-        scratch = '/scratch-ib'
     }
 
     debug { process.beforeScript = 'env' }

rain.nf

@@ -176,10 +176,10 @@ if ( ! (params.edit_site_tool in edit_site_tools) ){
 
 // check RAIN profile - /!\ profile must be sync with AliNe profile as much as possible
 if (
-    workflow.profile.contains('singularity') ||
-    workflow.profile.contains('docker')
+      workflow.containerEngine == "singularity" ||
+      workflow.containerEngine == "docker"
   ) { "executer selected" }
-else { exit 1, "No executer selected: -profile docker/singularity"}
+else { exit 1, "No executer selected: please use a profile activating docker or singularity (e.g. -profile docker/singularity/itrop)"}
 
 // check AliNE profile
 def aline_profile_list=[]
@@ -540,4 +540,4 @@ workflow.onComplete {
     =======================================================
     ${c_reset}
     """
-}
+}