Merge pull request #128 from nf-core/dev

Release 1.0.1

Author: nschan

.nf-core.yml

@@ -20,4 +20,4 @@ template:
   skip_features:
     - multiqc
     - igenomes
-  version: 1.0.0
+  version: 1.0.1

CHANGELOG.md

@@ -3,6 +3,22 @@
 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).
 
+## v1.0.1 'Aluminium Pigeon' - [2025-03.18]
+
+Bugfix release
+
+### `Added`
+
+### `Fixed`
+
+[#125](https://github.com/nf-core/genomeassembler/pull/125) - use correct genome-size for flye and longstitch.
+
+[#126](https://github.com/nf-core/genomeassembler/pull/126) - fixed wrong url for jellyfish singularity image.
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## v1.0.0 'Lead Pigeon' - [2025-03-07]
 
 Initial release of nf-core/genomeassembler, created with the [nf-core](https://nf-co.re/) template.

conf/modules.config

@@ -141,7 +141,7 @@ process {
     withName: FLYE {
         ext.args = {
             [
-                params.genome_size ? "--genome-size ${params.genome_size}" : '',
+                meta.genome_size ? "--genome-size ${meta.genome_size}" : '',
                 params.flye_args
             ].join(" ").trim()
         }

modules/local/jellyfish/dump/main.nf

@@ -2,7 +2,7 @@ process DUMP {
     tag "${meta.id}"
     label 'process_medium'
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/mer-jellyfish:2.3.1--h4ac6f70_0'
+        ? 'https://depot.galaxyproject.org/singularity/kmer-jellyfish:2.3.1--h4ac6f70_0'
         : 'biocontainers/kmer-jellyfish:2.3.1--h4ac6f70_0'}"
 
     input:

modules/local/jellyfish/histo/main.nf

@@ -2,7 +2,7 @@ process HISTO {
     tag "${meta.id}"
     label 'process_medium'
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/mer-jellyfish:2.3.1--h4ac6f70_0'
+        ? 'https://depot.galaxyproject.org/singularity/kmer-jellyfish:2.3.1--h4ac6f70_0'
         : 'biocontainers/kmer-jellyfish:2.3.1--h4ac6f70_0'}"
 
     input:

modules/local/jellyfish/stats/main.nf

@@ -2,7 +2,7 @@ process STATS {
     tag "${meta.id}"
     label 'process_medium'
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/mer-jellyfish:2.3.1--h4ac6f70_0'
+        ? 'https://depot.galaxyproject.org/singularity/kmer-jellyfish:2.3.1--h4ac6f70_0'
         : 'biocontainers/kmer-jellyfish:2.3.1--h4ac6f70_0'}"
 
     input:

modules/local/longstitch/main.nf

@@ -7,7 +7,7 @@ process LONGSTITCH {
         : 'biocontainers/longstitch:1.0.5--hdfd78af_0'}"
 
     input:
-    tuple val(meta), path(assembly), path(reads)
+    tuple val(meta), path(assembly), path(reads), val(genome_size)
 
     output:
     tuple val(meta), path("*.tigmint-ntLink-arks.fa"), emit: ntlLinks_arks_scaffolds
@@ -35,7 +35,7 @@ process LONGSTITCH {
         cp ${reads} reads.fq.gz
     fi
 
-    longstitch tigmint-ntLink-arks draft=assembly reads=reads t=${task.cpus} G=135e6 out_prefix=${prefix}
+    longstitch tigmint-ntLink-arks draft=assembly reads=reads t=${task.cpus} G=${genome_size} out_prefix=${prefix}
 
     mv *.tigmint-ntLink-arks.longstitch-scaffolds.fa ${prefix}.tigmint-ntLink-arks.fa
     sed -i 's/\\(scaffold[0-9]*\\),.*/\\1/' ${prefix}.tigmint-ntLink-arks.fa

nextflow.config

@@ -290,7 +290,7 @@ manifest {
     description     = """Assemble genomes from long ONT or pacbio HiFi reads"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '1.0.0'
+    version         = '1.0.1'
     doi             = '10.5281/zenodo.14986998'
 }
 

ro-crate-metadata.json

@@ -16,7 +16,7 @@ workflow ASSEMBLE {
     ont_reads // meta, reads
     hifi_reads // meta, reads
     ch_input
-    genomescope_out
+    genome_size
     meryl_kmers
 
     main:
@@ -57,13 +57,14 @@ workflow ASSEMBLE {
             }
             if (params.ont) {
                 ont_reads.set { flye_inputs }
-                if (params.genome_size == null && params.jellyfish) {
-                    params.genome_size = genomescope_out
-                }
             }
             // Run flye
+            flye_inputs
+                .join(genome_size)
+                .map { meta, reads, genomesize -> [meta +[ genome_size: genomesize ], reads] }
+                .set { flye_inputs }
             FLYE(flye_inputs, params.flye_mode)
-            FLYE.out.fasta.set { ch_assembly }
+            FLYE.out.fasta.map { meta, assembly -> [meta - meta.subMap('genome_size'), assembly] }.set { ch_assembly }
             ch_versions = ch_versions.mix(FLYE.out.versions)
         }
         if (params.assembler == "hifiasm") {
@@ -114,12 +115,14 @@ workflow ASSEMBLE {
             ch_versions = ch_versions.mix(HIFIASM.out.versions).mix(GFA_2_FA.out.versions)
 
             // Run flye
-            ont_reads.set { flye_inputs }
-            if (params.genome_size == null && params.jellyfish) {
-                params.genome_size = genomescope_out
-            }
+            ont_reads
+                .join(genome_size)
+                .map { meta, reads, genomesize -> [[id: meta.id, genome_size: genomesize], reads]}
+                .set { flye_inputs }
+
             FLYE(flye_inputs, params.flye_mode)
             FLYE.out.fasta
+                .map { meta, assembly -> [[id: meta.id], assembly] }
                 .join(
                     GFA_2_FA.out.contigs_fasta
                 )
@@ -148,7 +151,7 @@ workflow ASSEMBLE {
         Channel.empty().set { ch_ref_bam }
         if (params.assembler == "flye") {
             flye_inputs
-                .map { it -> [it[0], it[1]] }
+                .map { meta, reads -> [[id: meta.id], reads] }
                 .set { longreads }
         }
         if (params.assembler == "hifiasm" || params.assembler == "flye_on_hifiasm") {