Version bump and a couple of minor fixes

.github/version_checks.sh

@@ -1,5 +1,7 @@
 #!/usr/bin/env bash
 
+set -euo pipefail
+
 config_version=$(sed -n "/^\s*version\s*=\s*'/s/version//p" nextflow.config | tr -d "=[:space:]'")
 cff_version=$(sed -n '/^version: /s/version: //p' CITATION.cff | tr -d '[:space:]')
 

CHANGELOG.md

@@ -3,7 +3,7 @@
 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).
 
-## v2.2.0dev - [04-Nov-2024]
+## v2.2.0 - [04-Nov-2024]
 
 ### `Added`
 

CITATION.cff

@@ -25,7 +25,7 @@ authors:
   - family-names: "Deng"
     given-names: "Cecilia"
 title: "AssemblyQC: A Nextflow pipeline for reproducible reporting of assembly quality"
-version: 2.2.0dev
+version: 2.2.0
 date-released: 2024-07-30
 url: "https://github.com/Plant-Food-Research-Open/assemblyqc"
 doi: 10.1093/bioinformatics/btae477

modules/local/generatekaryotype.nf

@@ -35,8 +35,7 @@ process GENERATEKARYOTYPE {
         exit 0
     fi
 
-    tmp_file=\$(mktemp)
-    printf '%s\\n' "\${ref_seqs[@]}" > "\$tmp_file"
+    printf '%s\\n' "\${ref_seqs[@]}" > ${target_on_ref}.${seq_tag}.tmp
 
     if [[ $seq_tag = "all" ]];then
         cat $target_seq_len > filtered.target.seq.len
@@ -45,7 +44,7 @@ process GENERATEKARYOTYPE {
     fi
     cat filtered.target.seq.len | awk '{print \$1,\$2,"grey"}' OFS="\\t" > colored.filtered.target.seq.len
 
-    grep -w -f "\$tmp_file" $ref_seq_len > filtered.ref.seq.len
+    grep -w -f ${target_on_ref}.${seq_tag}.tmp $ref_seq_len > filtered.ref.seq.len
     cat filtered.ref.seq.len | awk '{print \$1,\$2,"black"}' OFS="\\t" > colored.filtered.ref.seq.len
 
     cat colored.filtered.ref.seq.len | sort -k1V > merged.seq.lengths
@@ -67,8 +66,6 @@ process GENERATEKARYOTYPE {
     | sed '/^\$/d' \
     | awk '{print "chr -",\$1,\$1,"0",\$2-1,\$3}' OFS="\\t" \
     > karyotype_target.tsv
-
-    rm "\$tmp_file"
     """
 
     stub:

nextflow.config

@@ -274,7 +274,7 @@ manifest {
     description     = """A Nextflow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '2.2.0dev'
+    version         = '2.2.0'
     doi             = 'https://doi.org/10.1093/bioinformatics/btae477'
 }