From 6c495dfb64cea5bd7c3c381bd792e65db9bfc64f Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Sun, 25 Apr 2021 17:07:19 +0200
Subject: [PATCH 1/2] Added --maxins for bt2

---
 CHANGELOG.md         | 2 ++
 main.nf              | 2 +-
 nextflow.config      | 1 +
 nextflow_schema.json | 9 ++++++++-
 4 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 87b4a9b68..c984c1f8b 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`
 
+- [#729](https://github.com/nf-core/eager/issues/729) Added Bowtie2 flag `--maxins` for PE mapping modern DNA mapping contexts 
+
 ### `Fixed`
 
 - Corrected explanation of the "--min_adap_overlap" parameter for AdapterRemoval in the docs
diff --git a/main.nf b/main.nf
index 6033028c6..44dee4d16 100644
--- a/main.nf
+++ b/main.nf
@@ -1357,7 +1357,7 @@ process bowtie2 {
     //PE data without merging, PE data without any AR applied
     if ( seqtype == 'PE' && ( params.skip_collapse || params.skip_adapterremoval ) ){
     """
-    bowtie2 -x ${fasta} -1 ${r1} -2 ${r2} -p ${task.cpus} ${sensitivity} ${bt2n} ${bt2l} ${trim5} ${trim3} --rg-id ILLUMINA-${libraryid} --rg SM:${libraryid} --rg PL:illumina --rg PU:ILLUMINA-${libraryid}-${seqtype} 2> "${libraryid}"_bt2.log | samtools sort -@ ${task.cpus} -O bam > "${libraryid}"_"${seqtype}".mapped.bam
+    bowtie2 -x ${fasta} -1 ${r1} -2 ${r2} -p ${task.cpus} ${sensitivity} ${bt2n} ${bt2l} ${trim5} ${trim3} --maxins ${bt2_maxins} --rg-id ILLUMINA-${libraryid} --rg SM:${libraryid} --rg PL:illumina --rg PU:ILLUMINA-${libraryid}-${seqtype} 2> "${libraryid}"_bt2.log | samtools sort -@ ${task.cpus} -O bam > "${libraryid}"_"${seqtype}".mapped.bam
     samtools index "${libraryid}"_"${seqtype}".mapped.bam ${size}
     """
     } else {
diff --git a/nextflow.config b/nextflow.config
index 5826e67f6..72127c379 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -89,6 +89,7 @@ params {
   bt2l = 0
   bt2_trim5 = 0
   bt2_trim3 = 0
+  bt2_maxins = 500
 
   //Mapped read removal from input FASTQ
   hostremoval_input_fastq = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 385c0d607..26a2fbf0f 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -634,6 +634,13 @@
                     "description": "Specify number of bases to trim off from 3' (right) end of read before alignment.",
                     "fa_icon": "fas fa-cut",
                     "help_text": "Number of bases to trim at the 3' (right) end of read prior alignment. Maybe useful when left-over sequencing artefacts of in-line barcodes present Default: 0.\n\n> Modifies Bowtie2 parameters: `-bt2_trim3`"
+                },
+                "bt2_maxins": {
+                    "type": "integer",
+                    "default": 500,
+                    "fa_icon": "fas fa-exchange-alt",
+                    "description": "Specify the maximum fragment length for Bowtie2 paired-end mapping mode only.",
+                    "help_text": "The maximum fragment for valid paired-end alignments. Only for paired-end mapping (i.e. unmerged), and therefore typically only useful for modern data.\n\n See [Bowtie2 documentation](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml) for more information.\n\n>  Modifies Bowtie2 parameters: `--maxins`"
                 }
             },
             "fa_icon": "fas fa-layer-group",
@@ -1642,4 +1649,4 @@
             "$ref": "#/definitions/metagenomic_authentication"
         }
     ]
-}
+}
\ No newline at end of file

From 16877229b7d14b112434c317d4c767e93ac98fb7 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Sun, 25 Apr 2021 17:10:08 +0200
Subject: [PATCH 2/2] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c984c1f8b..d1b9ea24a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Added`
 
-- [#729](https://github.com/nf-core/eager/issues/729) Added Bowtie2 flag `--maxins` for PE mapping modern DNA mapping contexts 
+- [#729](https://github.com/nf-core/eager/issues/729) Added Bowtie2 flag `--maxins` for PE mapping modern DNA mapping contexts
 
 ### `Fixed`