Release 1.8.8

CHANGELOG.md

@@ -1,4 +1,10 @@
 # Changelog
+## [v1.8.8]
+- Fix compatibility issues with NCBI datasets >= 14
+- Update documentation for iGenomes examples
+- Fix bug running a single alignment instance per genome
+    - The bug was linked to moving from `file` to `Channel`
+
 ## [v1.8.7]
 - Fixed a broken reference to `params.annotation` by using the new `params.annotation_format` instead
 - Add options to tweak minimap2 and GSAlign memory (e.g. `--gsalign_memory 6.GB` or `--minimap2_memory 8.GB`).

README.md

@@ -91,7 +91,7 @@ The source and target genomes can be specified as local or remote (un)compressed
 ### Download from NCBI
 *nf-LO* can download fasta files from ncbi directly using the [datasets API](https://www.ncbi.nlm.nih.gov/datasets/). Users provide a GCA/GCF code in the `--source`/`--target` field, and add the `--ncbi_source` and `--ncbi_target` flags as follow:
 ```
-nextflow run evotools/nf-LO --source "GCF_001549955.1" --target "GCF_011751205.1" --ncbi_source --ncbi_target  -profile conda 
+nextflow run evotools/nf-LO --source "GCF_001549955.1" --target "GCF_011751205.1" --ncbi_source --ncbi_target -profile conda 
 ```
 ### Download from iGenomes
 *nf-LO* can also download genomes from the [iGenomes](https://emea.support.illumina.com/sequencing/sequencing_software/igenome.html) site. Users provide a GCA/GCF code in the `--source`/`--target` field, and add the `--igenomes_source` and `--igenomes_target` flags as follow:

docs/alignments.md

@@ -90,8 +90,10 @@ Analogously, you can define the fragmentation of the source genome using:
 You can apply your own custom parameters to an alignment simply with the `--custom` flag:
 ```
 nextflow run evotools/nf-LO \
-   --igenome_source GRCh37 \
-   --igenome_target GRCh38 \
+   --source GRCh37 \
+   --target GRCh38 \
+   --igenome_source \
+   --igenome_target \
    --custom '-cx asm5 -l 10000' \
    --aligner minimap2  
 ``` 

environment.yml

@@ -11,7 +11,7 @@ dependencies:
   - last=1454
   - lastz=1.04.22
   - minimap2=2.28
-  - ncbi-datasets-cli=13.32.0
+  - ncbi-datasets-cli>13
   - p7zip=16.02
   - conda-forge::r-tidyverse=1.3.1
   - conda-forge::r-markdown=1.1

main.nf

@@ -114,8 +114,8 @@ no_maf          : $params.no_maf"""
         }
 
         DATA()
-        ch_source = DATA.out.ch_source
-        ch_target = DATA.out.ch_target
+        ch_source = DATA.out.ch_source | collect
+        ch_target = DATA.out.ch_target | collect
 
         // Preprocess the data
         preproc_ch = PREPROC( ch_source, ch_target )

modules/processes/datasets/main.nf

@@ -4,20 +4,20 @@ process dataset_genome {
     label "small"
 
     input:
-    val genome
+    val accession
 
     output:
-    path "${genome}.fasta"
+    path "${accession}.fasta"
 
     script:
     """
-    datasets download genome accession --exclude-rna --exclude-protein --exclude-protein --exclude-gff3 --exclude-genomic-cds ${genome} &&
-        7za x ncbi_dataset.zip && \
-        cat ncbi_dataset/data/${genome}/*.fna > ${genome}.fasta && rm -rf ncbi_dataset*
+    datasets download genome accession ${accession} --include genome && \\
+        7za x ncbi_dataset.zip && \\
+        cat ncbi_dataset/data/${accession}/*.fna > ${accession}.fasta && rm -rf ncbi_dataset*
     """
 
     stub:
     """
-    touch ${genome}.fasta
+    touch ${accession}.fasta
     """
 }