Merge pull request #111 from sanger-tol/bam_bugfix

Bugfix: the BAM still needs to be filtered with `-F0x400`

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

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"

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'
 }
 

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() )