From af37f1c69bcd3647fbd69deeff8ba3aef7457833 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Wed, 12 May 2021 10:14:32 +0200
Subject: [PATCH 1/2] Add reporting of location of multiqc run report on
 completeion

---
 CHANGELOG.md | 2 ++
 main.nf      | 1 +
 2 files changed, 3 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e68441280..9e073ac3f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Added`
 
+- [https://github.com/nf-core/eager/issues/736] - Add printing of multiqc run report location on successful completion
+
 ### `Fixed`
 
 ### `Dependencies`
diff --git a/main.nf b/main.nf
index 3473973ba..9745ed085 100644
--- a/main.nf
+++ b/main.nf
@@ -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}-"

From 08dc6abd9db8d7edeade728f274804716eb7343d Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Wed, 12 May 2021 10:30:42 +0200
Subject: [PATCH 2/2] Add bwa -o parameter as modifying is recommend for aDNA
 data according to latest simulation studies

---
 CHANGELOG.md         | 2 ++
 main.nf              | 8 ++++----
 nextflow.config      | 1 +
 nextflow_schema.json | 7 +++++++
 4 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e68441280..994c38740 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,8 @@ 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`
 
 ### `Fixed`
diff --git a/main.nf b/main.nf
index 3473973ba..e6d0ba5e4 100644
--- a/main.nf
+++ b/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}
     """
diff --git a/nextflow.config b/nextflow.config
index 40d3bb6c3..44786a02f 100644
--- a/nextflow.config
+++ b/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
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 3c05bdc51..a33f5455c 100644
--- a/nextflow_schema.json
+++ b/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,