Fix a regression, update README and call it 3.0.0

CHANGELOG.md

@@ -3,13 +3,14 @@
 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).
 
-## v2.1.0 - unreleased (tbd)
+## v3.0.0 - October 8th, 2024 (Chaenocephalus aceratus)
 
  - Run assemblyscan on the filtered genomes.
  - Allocate only a single CPU for 1 hour with 6 Gb memory for all computations.
  - Collect contig names to better check if sex chromosomes are missing from the assembly, etc.
  - Replace `seqkit` with shell commands and `seqtk` because of memory usage
    (https://github.com/shenwei356/seqkit/issues/487).
+   This changes directory and names of output files.
 
 ## v2.0.0 - September 24th, 2024 (Lama glama)
 

README.md

@@ -5,10 +5,10 @@
 **oist/LuscombeU_stlpreprocess** is a bioinformatics pipeline that ...
 
 1. Extract chromosomal scaffolds from the assembly file (discard unplaced, alternate, organelle sequences, etc.).
-2. Unmask the genome (to be re-masked later by another local pipeline.
-3. Extract mitochondrial genomes from the assembly file (they might be useful later as an internal control).
+2. Unmask the genome (to be re-masked later by another local pipeline).
+3. Extract complete mitochondrial genomes from the assembly file (they might be useful later as an internal control).
 4. Summarises the occurence of the first two letters of the accession numbers, to ease future changes of the grepping pattern for whole-chromosome scaffolds.
-5. Record the name of the extracted contigs, for instance to check if sex chromosomes are missing from the assembly.
+5. Record the name of the contigs, for instance to check if sex chromosomes are missing from the assembly.
 6. Show in the MultiQC report some assembly statistics such as GC content and contig length extracted with the <https://github.com/rpetit3/assembly-scan> software.
 
 ## Usage

modules/local/filter.nf

@@ -44,9 +44,11 @@ process FILTER {
         grep -i mitochondri |
         seqtk subseq $genome - | gzip --best --no-name > ${prefix}.mitogenome.fa.gz
 
-    # Remove outputs if empty (for some genomes the pattern does match chromosome-level scaffold accession numbers)
-    [ -z "\$(zcat ${prefix}.mitogenome.fa.gz  | head)" ] && rm ${prefix}.mitogenome.fa.gz
+    # Remove mitogenome file if containing less or more than one sequence
+    [ \$(zcat ${prefix}.mitogenome.fa.gz | grep -c '>') -ne 1 ] && rm ${prefix}.mitogenome.fa.gz
 
+    # Remove outputs if empty (for some genomes the pattern does match chromosome-level scaffold accession numbers)
+    # And then, remove soft masks.
     if [ -z "\$(zcat ${prefix}.chromosomes.fa.gz | head)" ]
     then
         rm ${prefix}.chromosomes.fa.gz