Merge pull request #115 from ewels/master

Strandedness - fixes and new additions

conf/uppmax.config

@@ -86,7 +86,7 @@ process {
   }
   $featureCounts {
     module = ['bioinfo-tools', 'subread/1.5.1']
-  }  
+  }
   $stringtieFPKM {
     module = ['bioinfo-tools', 'StringTie/1.3.3']
   }
@@ -108,7 +108,7 @@ params {
   clusterOptions = false
   rlocation = "$HOME/R/nxtflow_libs/"
   saveReference = true
-  reverse_stranded=true
+  reverse_stranded = true
   // illumina iGenomes reference file paths on UPPMAX
   genomes {
     'GRCh37' {

docs/usage.md

@@ -30,6 +30,29 @@ all files as single end. The file path should be in quotation marks to prevent s
 
 If left unspecified, the pipeline will assume that the data is in a directory called `data` in the working directory.
 
+### Library strandedness
+Three command line flags / config parameters set the library strandedness for a run:
+
+* `--forward_stranded`
+* `--reverse_stranded`
+* `--unstranded`
+
+If not set, the pipeline will be run as unstranded. The UPPMAX configuration file sets `reverse_stranded` to true by default.
+Use `--unstranded` or `--forward_stranded` to overwrite this.
+
+These flags affect the commands used for several steps in the pipeline - namely HISAT2, featureCounts, RSeQC (`RPKM_saturation.py`)
+and StringTie:
+* `--forward_stranded`
+  * HISAT2: `--rna-strandness F` / `--rna-strandness FR`
+  * featureCounts: `-s 1`
+  * RSeQC: `-d ++,--` / `-d 1++,1--,2+-,2-+`
+  * StringTie: `--fr`
+* `--reverse_stranded`
+  * HISAT2: `--rna-strandness R` / `--rna-strandness RF`
+  * featureCounts: `-s 2`
+  * RSeQC: `-d +-,-+` / `-d 1+-,1-+,2++,2--`
+  * StringTie: `--rf`
+
 ## Alignment tool
 By default, the pipeline uses [STAR](https://github.com/alexdobin/STAR) to align the raw FastQ reads
 to the reference genome. STAR is fast and common, but requires a great deal of RAM to run, typically
@@ -123,16 +146,6 @@ for common RNA-seq library preparation kits.
 | `--pico`  | SMARTer Stranded Total RNA-Seq Kit - Pico Input | 3     | 0     | 0     | 3     |
 
 
-### strand direction for StringTie and feturecounts
-The strandedness of the library can be set py using the `--forward_stranded`  and `--reverse_stranded` flags. Both are set as 
-`false` by default but reversed is set to true in the Uppmax config file. If you library instead is forward oriented simply specify the`--forward_stranded` flag. 
-
-e.g.
-```groovy
-`--forward_stranded` 
-```
-
-
 ## Job Resources
 ### Automatic resubmission
 Each step in the pipeline has a default set of requirements for number of CPUs,
@@ -170,24 +183,6 @@ The output directory where the results will be saved.
 ### `--sampleLevel`
 Used to turn of the edgeR MDS and heatmap. Set automatically when running on fewer than 3 samples.
 
-### `--strandRule`
-Some RSeQC jobs need to know the stranded nature of the library. By default, the pipeline will use
-`++,--` for single end libraries and `1+-,1-+,2++,2--` for paired end libraries. These codes are for
-strand specific libraries (antisense). `1+-,1-+,2++,2--` decodes as:
-
-*  Reads 1 mapped to `+` => parental gene on `+`
-*  Reads 1 mapped to `-` => parental gene on `-`
-*  Reads 2 mapped to `+` => parental gene on `-`
-*  Reads 2 mapped to `-` => parental gene on `+`
-
-Use this parameter to override these defaults. For example, if your data is paired end and strand specific,
-but same-sense to the reference, you could run:
-
-```bash
-nextflow run NGI-RNAseq/main.nf --strandRule '1++,1--,2+-,2-+'
-```
-Use `--strandRule 'none'` if your data is not strand specific.
-
 ### `--rlocation`
 Some steps in the pipeline run R with required modules. By default, the pipeline will install
 these modules to `~/R/nxtflow_libs/` if not present. You can specify what path to use with this

main.nf

@@ -11,8 +11,8 @@ vim: syntax=groovy
  #### Authors
  Phil Ewels @ewels <[email protected]>
  Rickard Hammarén @Hammarn  <[email protected]>
- Docker and AWS integration by 
- Denis Moreno @Galithil <[email protected]> 
+ Docker and AWS integration by
+ Denis Moreno @Galithil <[email protected]>
 ----------------------------------------------------------------------------------------
 */
 
@@ -29,6 +29,7 @@ params.project = false
 params.genome = false
 params.forward_stranded = false
 params.reverse_stranded = false
+params.unstranded = false
 params.star_index = params.genome ? params.genomes[ params.genome ].star ?: false : false
 params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
 params.gtf = params.genome ? params.genomes[ params.genome ].gtf ?: false : false
@@ -53,7 +54,6 @@ if (params.rlocation){
 
 def single
 params.sampleLevel = false
-params.strandRule = false
 
 // Custom trimming options
 params.clip_r1 = 0
@@ -140,6 +140,7 @@ if(params.aligner == 'star'){
 if(params.gtf)                 log.info "GTF Annotation : ${params.gtf}"
 else if(params.download_gtf)   log.info "GTF URL        : ${params.download_gtf}"
 if(params.bed12)               log.info "BED Annotation : ${params.bed12}"
+log.info "Strandedness   : ${params.unstranded ? 'None' : params.forward_stranded ? 'Forward' : params.reverse_stranded ? 'Reverse' : 'None'}"
 log.info "Current home   : $HOME"
 log.info "Current user   : $USER"
 log.info "Current path   : $PWD"
@@ -489,11 +490,18 @@ if(params.aligner == 'hisat2'){
         script:
         index_base = hs2_indices[0].toString() - ~/.\d.ht2/
         prefix = reads[0].toString() - ~/(_R1)?(_trimmed)?(_val_1)?(\.fq)?(\.fastq)?(\.gz)?$/
+        def rnastrandness = ''
+        if (params.forward_stranded && !params.unstranded){
+            rnastrandness = single ? '--rna-strandness F' : '--rna-strandness FR'
+        } else if (params.reverse_stranded && !params.unstranded){
+            rnastrandness = single ? '--rna-strandness R' : '--rna-strandness RF'
+        }
         if (single) {
             """
             set -o pipefail   # Capture exit codes from HISAT2, not samtools
             hisat2 -x $index_base \\
                    -U $reads \\
+                   $rnastrandness \\
                    --known-splicesite-infile $alignment_splicesites \\
                    -p ${task.cpus} \\
                    --met-stderr \\
@@ -506,6 +514,7 @@ if(params.aligner == 'hisat2'){
             hisat2 -x $index_base \\
                    -1 ${reads[0]} \\
                    -2 ${reads[1]} \\
+                   $rnastrandness \\
                    --known-splicesite-infile $alignment_splicesites \\
                    --no-mixed \\
                    --no-discordant \\
@@ -582,12 +591,12 @@ process rseqc {
 
     script:
     def strandRule = ''
-    if (params.forward_stranded){
-        strandRule = params.strandRule ?:  (single ? '-d +-,-+' : '-d 1+-,1-+,2++,2–')
-    } else if (params.reverse_stranded){
-        strandRule = params.strandRule ?: (single ? '-d ++,--' : '-d 1+-,1-+,2++,2--')
+    if (params.forward_stranded && !params.unstranded){
+        strandRule = single ? '-d ++,--' : '-d 1++,1--,2+-,2-+'
+    } else if (params.reverse_stranded && !params.unstranded){
+        strandRule = single ? '-d +-,-+' : '-d 1+-,1-+,2++,2--'
     }
-     """
+    """
     samtools index $bam_rseqc
     infer_experiment.py -i $bam_rseqc -r $bed12 > ${bam_rseqc.baseName}.infer_experiment.txt
     RPKM_saturation.py -i $bam_rseqc -r $bed12  $strandRule -o ${bam_rseqc.baseName}.RPKM_saturation
@@ -718,10 +727,10 @@ process featureCounts {
 
     script:
     def featureCounts_direction = 0
-    if (params.reverse_stranded){
-        featureCounts_direction = 2
-    } else if (params.forward_stranded) {
+    if (params.forward_stranded && !params.unstranded) {
         featureCounts_direction = 1
+    } else if (params.reverse_stranded && !params.unstranded){
+        featureCounts_direction = 2
     }
     """
     featureCounts -a $gtf -g gene_id -o ${bam_featurecounts.baseName}_gene.featureCounts.txt -p -s $featureCounts_direction $bam_featurecounts  
@@ -775,9 +784,9 @@ process stringtieFPKM {
 
     script:
     def StringTie_direction = ''
-    if (params.forward_stranded){
+    if (params.forward_stranded && !params.unstranded){
         StringTie_direction = "--fr"
-    } else if (!params.reverse_stranded){
+    } else if (!params.reverse_stranded && !params.unstranded){
         StringTie_direction = "--rf"
     }
     """