Merge pull request #16 from nf-core/dev

Get latest dev

CHANGELOG.md

@@ -5,8 +5,12 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## v2.3.5dev - [date]
 
+- [#722](https://github.com/nf-core/eager/issues/722) - Adds bwa `-o` flag for more flexibility in bwa parameters
+
 ### `Added`
 
+- [https://github.com/nf-core/eager/issues/736] - Add printing of multiqc run report location on successful completion
+
 ### `Fixed`
 
 - [#723](https://github.com/nf-core/eager/issues/723) - Fixes empty fields in TSV resulting in uninformative error

main.nf

@@ -1160,15 +1160,15 @@ process bwa {
     //PE data without merging, PE data without any AR applied
     if ( seqtype == 'PE' && ( params.skip_collapse || params.skip_adapterremoval ) ){
     """
-    bwa aln -t ${task.cpus} $fasta ${r1} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${libraryid}.r1.sai
-    bwa aln -t ${task.cpus} $fasta ${r2} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${libraryid}.r2.sai
+    bwa aln -t ${task.cpus} $fasta ${r1} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -o ${params.bwaalno} -f ${libraryid}.r1.sai
+    bwa aln -t ${task.cpus} $fasta ${r2} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -o ${params.bwaalno} -f ${libraryid}.r2.sai
     bwa sampe -r "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina\\tPU:ILLUMINA-${libraryid}-${seqtype}" $fasta ${libraryid}.r1.sai ${libraryid}.r2.sai ${r1} ${r2} | samtools sort -@ ${task.cpus} -O bam - > ${libraryid}_"${seqtype}".mapped.bam
     samtools index "${libraryid}"_"${seqtype}".mapped.bam ${size}
     """
     } else {
-    //PE collapsed, or SE data 
+    //PE collapsed, or SE data
     """
-    bwa aln -t ${task.cpus} ${fasta} ${r1} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${libraryid}.sai
+    bwa aln -t ${task.cpus} ${fasta} ${r1} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -o ${params.bwaalno} -f ${libraryid}.sai
     bwa samse -r "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina\\tPU:ILLUMINA-${libraryid}-${seqtype}" $fasta ${libraryid}.sai $r1 | samtools sort -@ ${task.cpus} -O bam - > "${libraryid}"_"${seqtype}".mapped.bam
     samtools index "${libraryid}"_"${seqtype}".mapped.bam ${size}
     """
@@ -3128,6 +3128,7 @@ workflow.onComplete {
 
     if (workflow.success) {
         log.info "-${c_purple}[nf-core/eager]${c_green} Pipeline completed successfully${c_reset}-"
+        log.info "-${c_purple}[nf-core/eager]${c_green} MultiQC run report can be found in ${params.outdir}/multiqc ${c_reset}-"
     } else {
         checkHostname()
         log.info "-${c_purple}[nf-core/eager]${c_red} Pipeline completed with errors${c_reset}-"

nextflow.config

@@ -80,6 +80,7 @@ params {
   bwaalnn = 0.04
   bwaalnk = 2
   bwaalnl = 1024 // From Schubert et al. 2012 (10.1186/1471-2164-13-178)
+  bwaalno = 1 // leave at bwa default for now
   circularextension = 500
   circulartarget = 'MT'
   circularfilter = false
@@ -394,7 +395,7 @@ manifest {
   homePage = 'https://github.com/nf-core/eager'
   description = 'A fully reproducible and state-of-the-art ancient DNA analysis pipeline'
   mainScript = 'main.nf'
-  nextflowVersion = '!>=20.07.1'
+  nextflowVersion = '>=20.07.1'
   version = '2.3.5dev'
 }
 

nextflow_schema.json

@@ -562,6 +562,13 @@
                     "fa_icon": "fas fa-ruler-horizontal",
                     "help_text": "Configures the length of the seed used in `bwa aln -l`. Default is set to be 'turned off' at the recommendation of Schubert et al. ([2012 _BMC Genomics_](https://doi.org/10.1186/1471-2164-13-178)) for ancient DNA with `1024`.\n\nNote: Despite being recommended, turning off seeding can result in long runtimes!\n\n> Modifies BWA aln parameter: `-l`\n"
                 },
+                "bwaalno": {
+                    "type": "integer",
+                    "default": 1,
+                    "fa_icon": "fas fa-people-arrows",
+                    "description": "Specify the -o parameter for BWA aln i.e. the number of gaps allowed.",
+                    "help_text": "Configures the number of gaps used in `bwa aln`. Default is set to `bwa` default.\n\n> Modifies BWA aln parameter: `-o`\n"
+                },
                 "circularextension": {
                     "type": "integer",
                     "default": 500,