v4.2.0 - November 21st, 2024 (Caenorhabditis inopinata)

CHANGELOG.md

@@ -3,6 +3,11 @@
 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).
 
+## v4.2.0 - November 21st, 2024 (Caenorhabditis inopinata)
+
+ - Allow `AP` and `BX` to rescue some Caenorhabditis assemblies.  `AP` rescues also
+   assemblies in various other clades.
+
 ## v4.1.0 - November 21st, 2024 (Sulfurisphaera ohwakuensis)
 
  - Allow `NC|NZ` in filtered contig names, for RefSeq assemblies.

README.md

@@ -63,6 +63,22 @@ scaffolds, plasmids and organelles almost exclusively. However there are excepti
  - _Brassica rapa_'s `GCA_900412535.3` uses `LS` for chromosomes and `OV` for shotgun
    scaffolds.
  - _Brassica oleracea_ `GCA_900416815`: `LS` / `OW`.
+ - _Strongyloides_ratti_GCA_001040885`: has only `LN` for both chromosome and
+   unplaced scaffold sequences.
+ - _Caenorhabditis inopinata_ `GCA_003052745.1`: `AP`.
+ - _Caenorhabditis elegans_ `GCA_000002985.3`: `BX`.
+
+To find the names of the genomes where nothing was extracted, try:
+
+```
+basename -s .patterns.txt *.patterns.txt | sed 's/$/.chromosomes_unmasked.fa.gz/' | xargs ls > /dev/null
+```
+
+To check if a new pattern would be suitable, try:
+
+```
+find . -name *patterns.txt | xargs grep -l AP | xargs head
+```
 
 ## Credits
 

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/oist/LuscombeU_stlpreprocess/releases/tag/4.1.0" target="_blank">oist/LuscombeU_stlpreprocess</a>
+  This report has been generated by the <a href="https://github.com/oist/LuscombeU_stlpreprocess/releases/tag/4.2.0" target="_blank">oist/LuscombeU_stlpreprocess</a>
   analysis pipeline.
 report_section_order:
   "oist-stlpreprocess-methods-description":

modules/local/filter.nf

@@ -41,7 +41,7 @@ process FILTER {
     sed 's/^>//' ${prefix}.contignames.txt |
         grep -vi -e mitochondri -e plasmid |
         awk '{print \$1}' |
-        grep -E "^(CM|CP|FR|L[R-T]|NC|NZ|O[U-Z])" > ${prefix}.contignames.chromosomes.txt ||
+        grep -E "^(AP|BX|CM|CP|FR|L[R-T]|NC|NZ|O[U-Z])" > ${prefix}.contignames.chromosomes.txt ||
         true > /dev/null # Returns success even if list is empty.
     samtools faidx -r ${prefix}.contignames.chromosomes.txt ${prefix}.orig_bgzipped.fa.gz | bgzip --threads $task.cpus --compress-level 9 > ${prefix}.chromosomes.fa.gz
 

nextflow.config

@@ -230,7 +230,7 @@ manifest {
     description     = """Download and pre-process genomes for the Scrambling in the Tree of Life project"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '4.1.0'
+    version         = '4.2.0'
     doi             = ''
 }