Merge pull request #128 from ewels/master

Bugfixing params overwriting and fixing --pico

CHANGELOG.md

@@ -1,10 +1,12 @@
 # NGI-RNAseq
 
-## 1.2dev
+## 1.2
 
 * MultiQC now runs using `local` instead of `slurm` with default config
   * Means that it stands a better chance of getting information from a remote database with plugins
 * MultiQC now uses the workflow name for report title and filename if specified
+* Fixed error where trimming parameters weren't set properly for `--pico`
+* Made pipeline run in forward-stranded mode when using `--pico`
 
 
 ## [1.1](https://github.com/SciLifeLab/NGI-RNAseq/releases/tag/1.1) - 2017-05-23

docs/usage.md

@@ -45,8 +45,7 @@ Three command line flags / config parameters set the library strandedness for a
 * `--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.
+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. Specifying `--pico` makes the pipeline run in `forward_stranded` mode.
 
 These flags affect the commands used for several steps in the pipeline - namely HISAT2, featureCounts, RSeQC (`RPKM_saturation.py`)
 and StringTie:
@@ -145,22 +144,30 @@ If specific additional trimming is required (for example, from additional tags),
 you can use any of the following command line parameters. These affect the command
 used to launch TrimGalore!
 
-* `--clip_r1 [int]`
-  * Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads).
-* `--clip_r2 [int]`
-  * Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only).
-* `--three_prime_clip_r1 [int]`
-  * Instructs Trim Galore to remove bp from the 3' end of read 1 _AFTER_ adapter/quality trimming has been performed.
-* `--three_prime_clip_r2 [int]`
-  * Instructs Trim Galore to re move bp from the 3' end of read 2 _AFTER_ adapter/quality trimming has been performed.
-
-### Trimming Presets
-Some command line options are available to automatically set these trimming parameters
-for common RNA-seq library preparation kits.
-
-| Parameter | Kit                                             | 5' R1 | 5' R2 | 3' R1 | 3' R2 |
-|-----------|-------------------------------------------------|-------|-------|-------|-------|
-| `--pico`  | SMARTer Stranded Total RNA-Seq Kit - Pico Input | 3     | 0     | 0     | 3     |
+### `--clip_r1 [int]`
+Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads).
+
+### `--clip_r2 [int]`
+Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only).
+
+### `--three_prime_clip_r1 [int]`
+Instructs Trim Galore to remove bp from the 3' end of read 1 _AFTER_ adapter/quality trimming has been performed.
+
+### `--three_prime_clip_r2 [int]`
+Instructs Trim Galore to re move bp from the 3' end of read 2 _AFTER_ adapter/quality trimming has been performed.
+
+
+## Library Prep Presets
+Some command line options are available to automatically set parameters for common RNA-seq library preparation kits.
+
+> Note that these presets override other command line arguments. So if you specify `--pico --clip_r1 0`, the `--clip_r1` bit will be ignored.
+
+If you have a kit that you'd like a preset added for, please let us know!
+
+### `--pico`
+Sets trimming and standedness settings for the _SMARTer Stranded Total RNA-Seq Kit - Pico Input_ kit.
+
+Equivalent to: `--forward_stranded` `--clip_r1 3` `--three_prime_clip_r2 3`
 
 
 ## Job Resources

main.nf

@@ -22,7 +22,7 @@ vim: syntax=groovy
  */
 
 // Pipeline version
-version = '1.1'
+version = '1.2'
 
 // Configurable variables
 params.name = false
@@ -65,13 +65,25 @@ params.clip_r2 = 0
 params.three_prime_clip_r1 = 0
 params.three_prime_clip_r2 = 0
 
+// Define regular variables so that they can be overwritten
+clip_r1 = params.clip_r1
+clip_r2 = params.clip_r2
+three_prime_clip_r1 = params.three_prime_clip_r1
+three_prime_clip_r2 = params.three_prime_clip_r2
+forward_stranded = params.forward_stranded
+reverse_stranded = params.reverse_stranded
+unstranded = params.unstranded
+
 // Preset trimming options
 params.pico = false
 if (params.pico){
-  params.clip_r1 = 3
-  params.clip_r2 = 0
-  params.three_prime_clip_r1 = 0
-  params.three_prime_clip_r2 = 3
+  clip_r1 = 3
+  clip_r2 = 0
+  three_prime_clip_r1 = 0
+  three_prime_clip_r2 = 3
+  forward_stranded = true
+  reverse_stranded = false
+  unstranded = false
 }
 
 // Choose aligner
@@ -148,8 +160,13 @@ def summary = [:]
 summary['Run Name']     = custom_runName ?: workflow.runName
 summary['Reads']        = params.reads
 summary['Data Type']    = params.singleEnd ? 'Single-End' : 'Paired-End'
-summary['Strandedness'] = ( params.unstranded ? 'None' : params.forward_stranded ? 'Forward' : params.reverse_stranded ? 'Reverse' : 'None' )
 summary['Genome']       = params.genome
+if( params.pico ) summary['Library Prep'] = "SMARTer Stranded Total RNA-Seq Kit - Pico Input"
+summary['Strandedness'] = ( unstranded ? 'None' : forward_stranded ? 'Forward' : reverse_stranded ? 'Reverse' : 'None' )
+summary['Trim R1'] = clip_r1
+summary['Trim R2'] = clip_r2
+summary["Trim 3' R1"] = three_prime_clip_r1
+summary["Trim 3' R2"] = three_prime_clip_r2
 if(params.aligner == 'star'){
     summary['Aligner'] = "STAR"
     if(params.star_index)          summary['STAR Index']   = params.star_index
@@ -166,21 +183,16 @@ if(params.aligner == 'star'){
 if(params.gtf)                 summary['GTF Annotation']  = params.gtf
 else if(params.download_gtf)   summary['GTF URL']         = params.download_gtf
 if(params.bed12)               summary['BED Annotation']  = params.bed12
+summary['Save Reference'] = params.saveReference
+summary['Save Trimmed']   = params.saveTrimmed
+summary['Save Intermeds'] = params.saveAlignedIntermediates
+summary['Output dir']     = params.outdir
+summary['Working dir']    = workflow.workDir
 summary['Current home']   = "$HOME"
 summary['Current user']   = "$USER"
 summary['Current path']   = "$PWD"
-summary['Working dir']    = workflow.workDir
-summary['Output dir']     = params.outdir
 summary['R libraries']    = params.rlocation
 summary['Script dir']     = workflow.projectDir
-summary['Save Reference'] = params.saveReference
-summary['Save Trimmed']   = params.saveTrimmed
-summary['Save Intermeds'] = params.saveAlignedIntermediates
-if( params.pico ) summary['Trim Profile'] = "SMARTer Stranded Total RNA-Seq Kit - Pico Input"
-if( params.clip_r1 > 0) summary['Trim R1'] = params.clip_r1
-if( params.clip_r2 > 0) summary['Trim R2'] = params.clip_r2
-if( params.three_prime_clip_r1 > 0) summary["Trim 3' R1"] = params.three_prime_clip_r1
-if( params.three_prime_clip_r2 > 0) summary["Trim 3' R2"] = params.three_prime_clip_r2
 summary['Config Profile'] = (workflow.profile == 'standard' ? 'UPPMAX' : workflow.profile)
 if(params.project) summary['UPPMAX Project'] = params.project
 if(params.email) summary['E-mail Address'] = params.email
@@ -415,10 +427,10 @@ process trim_galore {
     file "*_fastqc.{zip,html}" into trimgalore_fastqc_reports
 
     script:
-    c_r1 = params.clip_r1 > 0 ? "--clip_r1 ${params.clip_r1}" : ''
-    c_r2 = params.clip_r2 > 0 ? "--clip_r2 ${params.clip_r2}" : ''
-    tpc_r1 = params.three_prime_clip_r1 > 0 ? "--three_prime_clip_r1 ${params.three_prime_clip_r1}" : ''
-    tpc_r2 = params.three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${params.three_prime_clip_r2}" : ''
+    c_r1 = clip_r1 > 0 ? "--clip_r1 ${clip_r1}" : ''
+    c_r2 = clip_r2 > 0 ? "--clip_r2 ${clip_r2}" : ''
+    tpc_r1 = three_prime_clip_r1 > 0 ? "--three_prime_clip_r1 ${three_prime_clip_r1}" : ''
+    tpc_r2 = three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${three_prime_clip_r2}" : ''
     if (params.singleEnd) {
         """
         trim_galore --fastqc --gzip $c_r1 $tpc_r1 $reads
@@ -519,9 +531,9 @@ if(params.aligner == 'hisat2'){
         index_base = hs2_indices[0].toString() - ~/.\d.ht2/
         prefix = reads[0].toString() - ~/(_R1)?(_trimmed)?(_val_1)?(\.fq)?(\.fastq)?(\.gz)?$/
         def rnastrandness = ''
-        if (params.forward_stranded && !params.unstranded){
+        if (forward_stranded && !unstranded){
             rnastrandness = params.singleEnd ? '--rna-strandness F' : '--rna-strandness FR'
-        } else if (params.reverse_stranded && !params.unstranded){
+        } else if (reverse_stranded && !unstranded){
             rnastrandness = params.singleEnd ? '--rna-strandness R' : '--rna-strandness RF'
         }
         if (params.singleEnd) {
@@ -621,9 +633,9 @@ process rseqc {
 
     script:
     def strandRule = ''
-    if (params.forward_stranded && !params.unstranded){
+    if (forward_stranded && !unstranded){
         strandRule = params.singleEnd ? '-d ++,--' : '-d 1++,1--,2+-,2-+'
-    } else if (params.reverse_stranded && !params.unstranded){
+    } else if (reverse_stranded && !unstranded){
         strandRule = params.singleEnd ? '-d +-,-+' : '-d 1+-,1-+,2++,2--'
     }
     """
@@ -757,9 +769,9 @@ process featureCounts {
 
     script:
     def featureCounts_direction = 0
-    if (params.forward_stranded && !params.unstranded) {
+    if (forward_stranded && !unstranded) {
         featureCounts_direction = 1
-    } else if (params.reverse_stranded && !params.unstranded){
+    } else if (reverse_stranded && !unstranded){
         featureCounts_direction = 2
     }
     """
@@ -814,9 +826,9 @@ process stringtieFPKM {
 
     script:
     def st_direction = ''
-    if (params.forward_stranded && !params.unstranded){
+    if (forward_stranded && !unstranded){
         st_direction = "--fr"
-    } else if (params.reverse_stranded && !params.unstranded){
+    } else if (reverse_stranded && !unstranded){
         st_direction = "--rf"
     }
     """
@@ -962,6 +974,7 @@ workflow.onComplete {
     // Send the HTML e-mail
     if (params.email) {
         [ 'mail', '-s', subject, params.email ].execute() << email_html
+        log.info "[NGI-RNAseq] Sent summary e-mail to $params.email"
     }
 
     // Write summary e-mail HTML to a file
@@ -973,5 +986,6 @@ workflow.onComplete {
     output_f.withWriter { w ->
         w << email_html
     }
+    log.info "[NGI-RNAseq] Pipeline Complete"
 
 }