Fastqc

config/multiqc_conf.yml → config/multiqc_config.yaml

@@ -2,36 +2,21 @@ title: "RAIN report"
 
 run_modules:
     - fastqc
-    - bowtie2
-    - bwa 
-    - bwa-mem
-    - hisat2
-    - star
-    - picard/markdups
+    - picard
 
 module_order:
-    - fastqc:
-        name: FastQC (raw)
-        path_filters: 
-            - "*logs_raw*"
-    - bowtie2
-    - bwa 
-    - bwa-mem
-    - hisat2
-    - star
     - fastqc:
         name: FastQC (ali)
         path_filters: 
             - "*logs_ali*"
-    - picard/markdups
+    - picard:
+        path_filters: 
+            - "*marked_dup_metrics.txt"
     - fastqc:
         name: FastQC (markDuplicates)
         path_filters: 
             - "*logs_dup*"
     - fastqc:
         name: FastQC (ClipOverlap)
         path_filters: 
-            - "*logs_clip*"
-sp:
-  picard/markdups:
-    fn: "*marked_dup_metrics.txt"
+            - "*logs_clip*"

config/softwares.config

@@ -52,7 +52,9 @@ process {
         container = singularity.enabled ? "${params.sifPath}/sapin.sif" : "sapin"
     }
     withLabel: 'multiqc' {
-        container = 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0'
+        // container = 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0'
+        //container = 'quay.io/biocontainers/multiqc:1.27--pyhdfd78af_0'
+        container = 'quay.io/biocontainers/multiqc:1.28--pyhdfd78af_0'
     }
     withLabel: "pluviometer" {
         container = singularity.enabled ? "${params.sifPath}/pluviometer.sif" : "pluviometer"

modules/aline.nf

@@ -15,6 +15,7 @@ process AliNe {
         val read_type
         val aligner
         val library_type
+        val annotation
         val cache_dir          // String
 
     when:
@@ -34,11 +35,12 @@ process AliNe {
                 read_type,
                 aligner,
                 library_type,
+                "--annotation ${annotation}",
                 "--data_type rna",
                 "--outdir $task.workDir/AliNe",
         ].join(" ")
         // Copy command to shell script in work dir for reference/debugging.
-        file("$task.workDir/nf-cmd.sh").text = nxf_cmd.join(" ")
+        file("$task.workDir/nf-cmd.sh").text = nxf_cmd
         // Run nextflow command locally
         def process = nxf_cmd.execute(null, cache_path.toFile())
         process.waitFor()

modules/multiqc.nf

@@ -12,6 +12,6 @@ process multiqc {
 
     script:
         """
-        multiqc -p . -c ${multiqc_config}
+        multiqc . -c ${multiqc_config}
         """
 }

nextflow.config

@@ -59,7 +59,6 @@ profiles {
         includeConfig "$baseDir/config/resources/local.config"
     }
     test {
-        params.aline_profiles = "${baseDir}/config/resources/base_aline.config" 
         params.aligner        = "STAR" 
         params.reads          = "${baseDir}/data/chr21/chr21_small_R1.fastq.gz"
         params.genome         = "${baseDir}/data/chr21/chr21_small.fasta.gz"
@@ -68,7 +67,6 @@ profiles {
         params.read_type      = "short_single"
     }
     test2 {
-        params.aline_profiles = "${baseDir}/config/resources/base_aline.config" 
         params.aligner        = "STAR" 
         params.reads          = "${baseDir}/data/chr21/"
         params.genome         = "${baseDir}/data/chr21/chr21_small.fasta.gz" 

nextflow_aline.config

@@ -0,0 +1,42 @@
+// These are extra parameters specific to AliNe not handled by the RAIN pipeline
+
+params {
+
+    //   
+    samtools_stats     = false  // activate samtools stats
+    seqtk_sample_size  = 50000     // to change default AliNe sample size used to guess library type
+    read_length        = ""     // Used by star to set the sjdbOverhang parameter but also by some other aligners
+    relax              = ""     // 
+
+    // Aligner extra parameters
+    bbmap_options      = ''
+    bowtie_options     = ''
+    bowtie2_options    = ''
+    bwaaln_options     = ''
+    bwamem_options     = ''
+    bwamem2_options    = ''
+    bwasw_options      = ''
+    graphmap2_options  = '' // owler option is possible
+    hisat2_options     = ''
+    kallisto_options   = ''
+    kallisto_index_options = '' // e.g. to use --distinguish, --make-unique, etc...
+    last_options       = ''
+    last_index_options = ''
+    minimap2_options   = '' 
+    minimap2_index_options = '' //  -k, -w, -H and -I
+    ngmlr_options      = ''
+    novoalign_options  = ''
+    novoalign_license  = '' // license. You can ask for one month free trial license at http://www.novocraft.com/products/novoalign/
+    nucmer_options     = ''
+    salmon_options     = ''
+    salmon_index_options = ''
+    star_options       = ''
+    star_index_options = ''
+    star_2pass         = false
+    subread_options    = ''
+    sublong_options    = ''
+
+    // to store general information about pipeline execution
+    pipeline_report          = "pipeline_report"
+    monochrome_logs          = false
+}