Pre 1.3.1 PR (#5)

* Test conda changes

* Further conda test

* Update version in manifest

environments/squirrel.yml

@@ -0,0 +1,17 @@
+name: squirrel
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - biopython>=1.74
+  - minimap2>=2.16
+  - python=3.10
+  - snakemake-minimal=7.32
+  - matplotlib>=3.3.1
+  - gofasta
+  - iqtree>=2.1
+  - jclusterfunk>=0.0.25
+  - pip
+  - pip:
+    - git+https://github.com/aineniamh/squirrel.git@main

lib/WorkflowMain.groovy

@@ -53,12 +53,12 @@ class WorkflowMain {
         // Explode on conda
         // conda.enabled seems to be backward compatible but wrap this
         // in a generic catch just in case
-        try {
-            if (workflow.session.config.conda.enabled) {
-                log.error "Sorry, this workflow is not compatible with Conda, please use -profile standard (Docker) or -profile singularity."
-                System.exit(1)
-            }
-        } catch(Exception e) {}
+        // try {
+        //     if (workflow.session.config.conda.enabled) {
+        //         log.error "Sorry, this workflow is not compatible with Conda, please use -profile standard (Docker) or -profile singularity."
+        //         System.exit(1)
+        //     }
+        // } catch(Exception e) {}
 
         // Validate workflow parameters via the JSON schema
         if (params.validate_params) {

modules/illumina.nf

@@ -52,7 +52,7 @@ process align_trim {
 
     container 'community.wave.seqera.io/library/pysam_samtools_numpy_pandas:0ef969f9a905399f'
 
-    conda 'bioconda::pysam=0.22.1', 'bioconda::samtools=1.12', 'conda-forge::numpy=2.1.1', 'conda-forge::pandas=2.2.2'
+    conda 'bioconda::pysam=0.22.1 bioconda::samtools=1.12 conda-forge::numpy=2.1.1 conda-forge::pandas=2.2.2'
 
     publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "${sampleName}.primertrimmed.rg.sorted.bam*", mode: 'copy'
     publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "${sampleName}.amplicon_depths.tsv", mode: 'copy'
@@ -94,7 +94,7 @@ process indexReference {
 
     container 'community.wave.seqera.io/library/bwa:0.7.18--324359fbc6e00dba'
 
-    conda 'bioconda::bwa=0.7.17'
+    conda 'bioconda::bwa=0.7.18'
 
     input:
     path(ref)
@@ -122,7 +122,7 @@ process readMapping {
 
     container 'community.wave.seqera.io/library/bwa_samtools:3938c84206f62975'
 
-    conda 'bioconda::bwa=0.7.18', 'bioconda::samtools=1.12'
+    conda 'bioconda::bwa=0.7.18 bioconda::samtools=1.12'
 
     publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "${sampleName}.sorted{.bam,.bam.bai}", mode: 'copy'
 
@@ -149,7 +149,7 @@ process callConsensusFreebayes {
 
     container 'community.wave.seqera.io/library/bcftools_freebayes_pysam_tabix:c16cddc9a1a28b82'
 
-    conda 'bioconda::freebayes=1.3.6', 'bioconda::bcftools=1.20', 'bioconda::pysam=0.22.1', 'bioconda::tabix=1.11'
+    conda 'bioconda::freebayes=1.3.6 bioconda::bcftools=1.20 bioconda::pysam=0.22.1 bioconda::tabix=1.11'
 
     publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "${sampleName}.consensus.fa", mode: 'copy'
     publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "${sampleName}.variants.norm.vcf", mode: 'copy'

modules/qc.nf

@@ -6,7 +6,7 @@ process makeQCCSV {
 
     container 'community.wave.seqera.io/library/samtools_biopython_matplotlib_pandas:2bb143fe29dc1ce9'
 
-    conda "conda-forge::matplotlib=3.9.2", "conda-forge::pandas=2.2.2", "conda-forge::biopython=1.84", "bioconda::samtools=1.20"
+    conda "conda-forge::matplotlib=3.9.2 conda-forge::pandas=2.2.2 conda-forge::biopython=1.84 bioconda::samtools=1.20"
 
     publishDir "${params.outdir}/qc_plots", pattern: "${sampleName}.depth.png", mode: 'copy'
 

modules/squirrel.nf

@@ -4,6 +4,8 @@ process squirrelAlignmentAndQC {
 
     container "docker.io/articnetworkorg/squirrel@sha256:78921da0c726dd525f5d72db331526975adb634478ee31047c46765bd3d5a64a"
 
+    conda "${projectDir}/environments/squirrel.yml"
+
     publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "squirrel/**", mode: 'copy', saveAs: {  fn -> fn.replace("squirrel/", "")}
 
     input:

modules/utils.nf

@@ -1,67 +1,3 @@
-process articDownloadScheme{
-    tag params.schemeRepoURL
-
-    label 'internet'
-
-    publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "scheme", mode: "copy"
-
-    output:
-    path "scheme/**/${params.schemeVersion}/*.reference.fasta" , emit: reffasta
-    path "scheme/**/${params.schemeVersion}/${params.scheme}.bed" , emit: bed
-    path "scheme" , emit: scheme
-
-    script:
-    """
-    git clone ${params.schemeRepoURL} scheme
-    """
-}
-
-process get_bed_ref {
-
-    label 'process_single'
-
-    container 'nextflow/bash:latest'
-
-    input:
-        path scheme_dir
-        val scheme_name
-        val scheme_version
-    output:
-        path "primer.bed", emit: bed
-        path "reference.fasta", emit: ref
-        path "reference.gff3", emit: gff
-
-    """
-    cp ${scheme_name}/${scheme_version}/primer.bed primer.bed
-    cp ${scheme_name}/${scheme_version}/reference.fasta reference.fasta
-    cp ${scheme_name}/${scheme_version}/reference.gff3 reference.gff3
-    """
-}
-
-process performHostFilter {
-
-    tag { sampleName }
-
-    container 'community.wave.seqera.io/library/bwa_pysam_samtools_python:f3b7e3fe2ad2cadc'
-
-    conda 'bioconda::bwa=0.7.18', 'bioconda::samtools=1.20', 'bioconda::python=3.12.5', 'bioconda::pysam=0.22.1'
-
-    publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "${sampleName}_hostfiltered_R*.fastq.gz", mode: 'copy'
-
-    input:
-        tuple val(sampleName), path(forward), path(reverse)
-    output:
-        tuple val(sampleName), path("${sampleName}_hostfiltered_R1.fastq.gz"), path("${sampleName}_hostfiltered_R2.fastq.gz"), emit: fastqPairs
-
-    script:
-        """
-        bwa mem -t ${task.cpus} ${params.composite_ref} ${forward} ${reverse} | \
-            filter_non_human_reads.py -c ${params.viral_contig_name} > ${sampleName}.viral_and_nonmapping_reads.bam
-        samtools sort -n ${sampleName}.viral_and_nonmapping_reads.bam | \
-             samtools fastq -1 ${sampleName}_hostfiltered_R1.fastq.gz -2 ${sampleName}_hostfiltered_R2.fastq.gz -s ${sampleName}_singletons.fastq.gz -
-        """
-}
-
 process publish {
     publishDir "${params.outdir}/", mode: 'copy'
     container 'nextflow/bash:latest'

nextflow.config

@@ -5,7 +5,7 @@ manifest {
   description = 'Epi2me compatible Nextflow pipeline for processing ARTIC tiling amplicon Illumina sequencing reads from monkeypox virus (MPXV) samples.'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.01.0'
-  version = '1.3.0'
+  version = '1.3.1'
   defaultBranch = 'main'
 }