Delete mitogenome files that contain more than one sequence.

CHANGELOG.md

@@ -3,22 +3,15 @@
 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).
 
-## unreleased
+## v2.0.0 - September 24th, 2024 (Lama glama)
 
-Allow TSV format and change column names to `id` and `file`.
+ - Allow TSV format and change column names to `id` and `file`.
+ - Delete mitogenome files that contain more than one sequence.
 
 ## v1.1.0 - September 24th, 2024 (Mus caroli)
 
-Expanded the pattern matching chromosome contigs to `^(CM|CP|FR|L[R-T]|O[U-Z])`.
+ - Expanded the pattern matching chromosome contigs to `^(CM|CP|FR|L[R-T]|O[U-Z])`.
 
 ## v1.0.0 - September 20th, 2024 (Orang Outan)
 
-Initial release of oist/LuscombeU_stlpreprocess, created with the [nf-core](https://nf-co.re/) template.
-
-### `Added`
-
-### `Fixed`
-
-### `Dependencies`
-
-### `Deprecated`
+ - Initial release of oist/LuscombeU_stlpreprocess, created with the [nf-core](https://nf-co.re/) template.

README.md

@@ -9,17 +9,6 @@
 3. Extract 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.
 
-## TODO
-
-- Some assemblies only contain fragmented condigs of the mitochondrial genome.
-  Filter them out.
-   - In `GCA_000146795` they match `Contig` and `>AD` while
-     complete Primate mitogenomes do not (`>CM`, `>CP`, `>J0`, `>KT`, `>LN`).
-   - In `GCA_015711505` they match `HiC_scaffold` and `>JA` while
-     complete Glire mitogenomes do not (`>AA`, `>AY`, `>CM`, `>JA`, `>LR`, `>OR`, `>OW`, `>OX`, `>OY`, `>OZ`).
-   - In `GCA_019903745` they match `>JA`, while no other Artiodactyla does.
-  This said, maybe it will be easier to just delete files that contain more than one sequence?
-
 ## Usage
 
 > [!NOTE]

assets/samplesheet.tsv

@@ -1,3 +1,4 @@
 id	file	other
 GRCh38	assets/GRCh38.head.fa.gz	unused column
-mitoch	assets/GRCh38.mito.fa.gz	added for tests
+mito_1	assets/GRCh38.mito1.fa.gz	added for tests
+mito_2	assets/GRCh38.mito2.fa.gz	…

modules/local/mitogenome.nf

@@ -31,8 +31,8 @@ process MITOGENOME {
         ${sequence} \\
         -o ${prefix}.mitogenome.${suffix}.gz \\
 
-    # Remove output if empty
-    [ -z "\$(zcat ${prefix}.mitogenome.${suffix}.gz | head)" ] && rm ${prefix}.mitogenome.${suffix}.gz
+    # Remove if containing less or more than one sequence
+    [ \$(zcat ${prefix}.mitogenome.${suffix}.gz | grep -c '>') -ne 1 ] && rm ${prefix}.mitogenome.${suffix}.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":