From 5e5a8bd152914dcee046fedcc396da41687f4ae9 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Fri, 26 Apr 2024 17:04:30 +0000
Subject: [PATCH 1/2] Bugfix: the BAM still needs to be filtered with `-F0x400`

---
 subworkflows/local/contact_maps.nf | 16 ++--------------
 1 file changed, 2 insertions(+), 14 deletions(-)

diff --git a/subworkflows/local/contact_maps.nf b/subworkflows/local/contact_maps.nf
index b1c316f3..4e802d83 100644
--- a/subworkflows/local/contact_maps.nf
+++ b/subworkflows/local/contact_maps.nf
@@ -34,30 +34,18 @@ workflow CONTACT_MAPS {
     FILTER_GENOME ( SAMTOOLS_FAIDX.out.fai )
     ch_versions = ch_versions.mix ( FILTER_GENOME.out.versions.first() )
 
-    // Separate CRAM from BAM
-    reads
-    | branch { meta, file, index ->
-        bam : file.extension == "bam"
-                [meta, file]
-        cram: file.extension == "cram"
-    }
-    | set { ch_reads }
 
     // CRAM to BAM
     genome
     | map { meta, fasta -> fasta }
     | set { ch_fasta }
 
-    SAMTOOLS_VIEW ( ch_reads.cram, ch_fasta, [] )
+    SAMTOOLS_VIEW ( reads, ch_fasta, [] )
     ch_versions = ch_versions.mix ( SAMTOOLS_VIEW.out.versions.first() )
 
-    // BAM reads
-    ch_reads.bam
-    | mix ( SAMTOOLS_VIEW.out.bam )
-    | set { ch_reads_bam }
 
     // BAM to Bed
-    BEDTOOLS_BAMTOBED ( ch_reads_bam )
+    BEDTOOLS_BAMTOBED ( SAMTOOLS_VIEW.out.bam )
     ch_versions = ch_versions.mix ( BEDTOOLS_BAMTOBED.out.versions.first() )
 
 

From 58a58ff228c8bc7ae7dbaf9ddb47369a6f42cf9d Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Sat, 27 Apr 2024 18:51:30 +0000
Subject: [PATCH 2/2] Version bump

---
 CHANGELOG.md    | 6 ++++++
 CITATION.cff    | 4 ++--
 nextflow.config | 2 +-
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 55b280c7..5aeb7560 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[1.1.2](https://github.com/sanger-tol/genomenote/releases/tag/1.1.2)] [2024-04-29]
+
+### Enhancements & fixes
+
+- Bugfix: the BAM still needs to be filtered with `-F0x400`
+
 ## [[1.1.1](https://github.com/sanger-tol/genomenote/releases/tag/1.1.1)] [2024-02-26]
 
 ### Enhancements & fixes
diff --git a/CITATION.cff b/CITATION.cff
index afe55544..0b466326 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -2,7 +2,7 @@
 # Visit https://bit.ly/cffinit to generate yours today!
 
 cff-version: 1.2.0
-title: sanger-tol/genomenote v1.1.1
+title: sanger-tol/genomenote v1.1.2
 message: >-
     If you use this software, please cite it using the
     metadata from this file.
@@ -34,5 +34,5 @@ identifiers:
 repository-code: "https://github.com/sanger-tol/genomenote"
 license: MIT
 commit: TODO
-version: 1.1.1
+version: 1.1.2
 date-released: "2022-10-07"
diff --git a/nextflow.config b/nextflow.config
index 346afe1f..1a6281d8 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -221,7 +221,7 @@ manifest {
     description     = """Creating standarised genome assembly publications"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.1.1'
+    version         = '1.1.2'
     doi             = '10.5281/zenodo.7949384'
 }