From b58ae39dc8ac53f325e0e0d61e9cb2af99513a4f Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 24 Mar 2022 10:32:18 +0100
Subject: [PATCH 1/3] Fix bwa mem indexing and re-update MQC SeqTools versions
 after git mess this morning

---
 CHANGELOG.md    | 1 +
 environment.yml | 4 ++--
 main.nf         | 2 +-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 612a91836..7d93847a1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - Renamed a range of MultiQC general stats table headers to improve clarity, documentation has been updated accordingly
 - [#857](https://github.com/nf-core/eager/issues/857) Corrected samtools fastq flag to _retain_ read-pair information when converting off-target BAM files to fastq in paired-end mapping (❤ to @alexhbnr for reporting)
 - [#858](https://github.com/nf-core/eager/pull/858) Corrected tutorials to reflect updated BAM trimming flags (❤ to @marcel-keller for reporting)
+- [#858](https://github.com/nf-core/eager/pull/858) Corrected tutorials to reflect updated BAM trimming flags (❤ to @marcel-keller for reporting)
 
 ### `Dependencies`
 
diff --git a/environment.yml b/environment.yml
index 39d8ce233..2a0230cdf 100644
--- a/environment.yml
+++ b/environment.yml
@@ -26,12 +26,12 @@ dependencies:
   - bioconda::qualimap=2.2.2d
   - bioconda::vcf2genome=0.91
   - bioconda::damageprofiler=0.4.9 # Don't upgrade - later versions don't allow java 8
-  - bioconda::multiqc=1.11
+  - bioconda::multiqc=1.12
   - bioconda::pmdtools=0.60
   - bioconda::bedtools=2.30.0
   - conda-forge::libiconv=1.16
   - conda-forge::pigz=2.6
-  - bioconda::sequencetools=1.4.0.6
+  - bioconda::sequencetools=1.5.2
   - bioconda::preseq=3.1.2
   - bioconda::fastp=0.20.1
   - bioconda::bamutil=1.0.15
diff --git a/main.nf b/main.nf
index afd26d4db..bca681bd2 100644
--- a/main.nf
+++ b/main.nf
@@ -1318,7 +1318,7 @@ process bwamem {
     if (!params.single_end && params.skip_collapse){
     """
     bwa mem -t ${split_cpus} $fasta $r1 $r2 -R "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${samplename}\\tPL:illumina\\tPU:ILLUMINA-${libraryid}-${seqtype}" | samtools sort -@ ${split_cpus} -O bam - > "${libraryid}"_"${seqtype}".mapped.bam
-    samtools index ${size} -@ ${task.cpus} "${libraryid}".mapped.bam
+    samtools index ${size} -@ ${task.cpus} "${libraryid}"_"${seqtype}".mapped.bam
     """
     } else {
     """

From 01655ee3d261a53e72c46c4bf12f87eb769dcef6 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 24 Mar 2022 10:36:29 +0100
Subject: [PATCH 2/3] Update changelog and update test

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7d93847a1..cec43aeef 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,7 +19,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - Renamed a range of MultiQC general stats table headers to improve clarity, documentation has been updated accordingly
 - [#857](https://github.com/nf-core/eager/issues/857) Corrected samtools fastq flag to _retain_ read-pair information when converting off-target BAM files to fastq in paired-end mapping (❤ to @alexhbnr for reporting)
 - [#858](https://github.com/nf-core/eager/pull/858) Corrected tutorials to reflect updated BAM trimming flags (❤ to @marcel-keller for reporting)
-- [#858](https://github.com/nf-core/eager/pull/858) Corrected tutorials to reflect updated BAM trimming flags (❤ to @marcel-keller for reporting)
+- [#866](https://github.com/nf-core/eager/issues/866) Fixed a typo in the indexing step of BWA mem when not-collapsing (❤ to @alexhbnr for reporting)
 
 ### `Dependencies`
 

From 5f85ee66f8171ca2f7f3ea913f1d6e1dd10e146a Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 24 Mar 2022 11:15:56 +0100
Subject: [PATCH 3/3] Add skip collapse flag..

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 599fd53af..afefa04c9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -119,7 +119,7 @@ jobs:
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'circularmapper' --circulartarget 'NC_007596.2'
       - name: MAPPER_BWAMEM Test running with BWA Mem
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'bwamem'
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'bwamem' --skip_collapse
       - name: MAPPER_BT2 Test running with BowTie2
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'bowtie2' --bt2_alignmode 'local' --bt2_sensitivity 'sensitive' --bt2n 1 --bt2l 16 --bt2_trim5 1 --bt2_trim3 1