bambu 3.2.4 & bam inputs for DNA variant calling

conf/test_nobc_nodx_noaln_vc.config

@@ -0,0 +1,30 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/nanoseq -profile test_nobc_nodx_vc,<docker/singularity>
+ */
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check variant calling functions'
+
+    // Limit resources so that this can run on Travis
+    max_cpus            = 2
+    max_memory          = 6.GB
+    max_time            = 12.h
+
+    // Input data to skip demultiplexing and variant call
+    input               = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/nanoseq/3.2/samplesheet/samplesheet_nobc_nodx_noaln_vc.csv'
+    fasta               = 'https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/reference/hg19_KCMF1.fa'
+    skip_basecalling    = true
+    protocol            = 'DNA'
+    skip_alignment      = true
+    skip_quantification = true
+    skip_demultiplexing = true
+    call_variants       = true
+    variant_caller      = 'clair3'
+    structural_variant_caller = 'sniffles'
+}

modules/local/bambu.nf

@@ -3,8 +3,8 @@ process BAMBU {
 
     conda "conda-forge::r-base=4.0.3 bioconda::bioconductor-bambu=3.0.8 bioconda::bioconductor-bsgenome=1.66.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-bambu:3.0.8--r42hc247a5b_0' :
-        'quay.io/biocontainers/bioconductor-bambu:3.0.8--r42hc247a5b_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-bambu:3.2.4--r43hf17093f_0' :
+        'quay.io/biocontainers/bioconductor-bambu:3.2.4--r43hf17093f_0' }"
 
     input:
     tuple path(fasta), path(gtf)

modules/local/blue-crab.nf

@@ -0,0 +1,29 @@
+process BLUE_CRAB {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "bioconda::slow5tools==1.2.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/slow5tools:1.2.0--h56e2c18_1' :
+        'quay.io/biocontainers/slow5tools:1.2.0--h56e2c18_1' }"
+
+    input:
+    tuple val(meta), path(genome), path(gtf), path(fastq), path(bam), path(bai), path(pod5)
+
+    output:
+    tuple val(meta), path(genome), path(gtf), path(fastq), path(bam), path(bai), path(blow5), emit: nanopolish_outputs
+    path "versions.yml"                                                                     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    """
+    blue-crab p2s $pod5 -o $blow5
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        blue-crab: \$( blue-crab -V | tail -c 6 )
+    END_VERSIONS
+    """
+}

modules/local/modkit_bedmethyl.nf

@@ -0,0 +1,27 @@
+process DORADO {
+    tag "$meta.id"
+    label 'process_medium'
+
+    container "modkit"
+
+    input:
+    tuple val(meta), path(mod_bam)
+
+    output:
+    tuple val(meta), path("*.bed") , emit: bedmethyl
+    path "versions.yml"                  , emit: versions
+
+    script:
+    bedmethyl = "$meta.id" +".bed"
+    """
+    modkit pileup $mod_bam $bedmethyl
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        dorado: \$(echo \$(dorado --version 2>&1) | sed -r 's/.{81}//')
+    END_VERSIONS
+
+    gzip basecall.fastq
+    """
+}
+

nextflow.config

@@ -231,6 +231,7 @@ profiles {
     test_nobc_nodx_stringtie { includeConfig 'conf/test_nobc_nodx_stringtie.config' }
     test_nobc_nodx_noaln     { includeConfig 'conf/test_nobc_nodx_noaln.config'     }
     test_nobc_nodx_vc        { includeConfig 'conf/test_nobc_nodx_vc.config'        }
+    test_nobc_nodx_noaln_vc  { includeConfig 'conf/test_nobc_nodx_noaln_vc.config'  }
     test_nobc_nodx_rnamod    { includeConfig 'conf/test_nobc_nodx_rnamod.config'    }
 }
 

workflows/nanoseq.nf

@@ -152,6 +152,7 @@ include { QCAT                        } from '../modules/nf-core/qcat/main'
 include { NANOLYSE                    } from '../modules/nf-core/nanolyse/main'
 include { CUSTOM_GETCHROMSIZES        } from '../modules/nf-core/custom/getchromsizes/main'
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
+include { SAMTOOLS_INDEX              } from '../modules/nf-core/samtools/index/main'
 
 /*
  * SUBWORKFLOW: Consisting entirely of nf-core/modules
@@ -335,18 +336,18 @@ workflow NANOSEQ{
         ch_fastqc_multiqc    = QCFASTQ_NANOPLOT_FASTQC.out.fastqc_multiqc.ifEmpty([])
     }
 
-    ch_samtools_multiqc = Channel.empty()
-    if (!params.skip_alignment) {
+    ch_fasta = Channel.from( [id:'reference'], fasta ).collect()
 
-        ch_fasta = Channel.from( [id:'reference'], fasta ).collect()
+    /*
+        * SUBWORKFLOW: Make chromosome size file and covert GTF to BED12
+        */
+    CUSTOM_GETCHROMSIZES( ch_fasta )
+    ch_chr_sizes         = CUSTOM_GETCHROMSIZES.out.sizes
+    ch_fai               = CUSTOM_GETCHROMSIZES.out.fai
+    ch_software_versions = ch_software_versions.mix(CUSTOM_GETCHROMSIZES.out.versions.first().ifEmpty(null))
 
-        /*
-         * SUBWORKFLOW: Make chromosome size file and covert GTF to BED12
-         */
-        CUSTOM_GETCHROMSIZES( ch_fasta )
-        ch_chr_sizes         = CUSTOM_GETCHROMSIZES.out.sizes
-        ch_fai               = CUSTOM_GETCHROMSIZES.out.fai
-        ch_software_versions = ch_software_versions.mix(CUSTOM_GETCHROMSIZES.out.versions.first().ifEmpty(null))
+    ch_samtools_multiqc = Channel.empty()
+    if (!params.skip_alignment) {
 
         if (params.aligner == 'minimap2') {
 
@@ -370,25 +371,6 @@ workflow NANOSEQ{
             ch_software_versions = ch_software_versions.mix(ALIGN_GRAPHMAP2.out.samtools_version.first().ifEmpty(null))
         }
 
-        if (params.call_variants && params.protocol == 'DNA') {
-
-            /*
-            * SUBWORKFLOW: Short variant calling
-            */
-            if (!params.skip_vc) {
-                SHORT_VARIANT_CALLING ( ch_sorted_bam, ch_sorted_bai, ch_fasta, ch_fai )
-                ch_software_versions = ch_software_versions.mix(SHORT_VARIANT_CALLING.out.ch_versions.first().ifEmpty(null))
-            }
-
-            /*
-            * SUBWORKFLOW: Structural variant calling
-            */
-            if (!params.skip_sv) {
-                STRUCTURAL_VARIANT_CALLING ( ch_sorted_bam, ch_sorted_bai, ch_fasta, ch_fai )
-                ch_software_versions = ch_software_versions.mix(STRUCTURAL_VARIANT_CALLING.out.ch_versions.first().ifEmpty(null))
-            }
-        }
-
         ch_bedtools_version = Channel.empty()
         if (!params.skip_bigwig) {
 
@@ -420,6 +402,29 @@ workflow NANOSEQ{
         ch_sorted_bam = BAM_RENAME.out.bam
     }
 
+    if (params.call_variants && params.protocol == 'DNA') {
+
+        SAMTOOLS_INDEX ( ch_sorted_bam )
+        ch_sorted_bai = SAMTOOLS_INDEX.out.bai
+        samtools_version = SAMTOOLS_INDEX.out.versions
+
+        /*
+        * SUBWORKFLOW: Short variant calling
+        */
+        if (!params.skip_vc) {
+            SHORT_VARIANT_CALLING ( ch_sorted_bam, ch_sorted_bai, ch_fasta, ch_fai )
+            ch_software_versions = ch_software_versions.mix(SHORT_VARIANT_CALLING.out.ch_versions.first().ifEmpty(null))
+        }
+
+        /*
+        * SUBWORKFLOW: Structural variant calling
+        */
+        if (!params.skip_sv) {
+            STRUCTURAL_VARIANT_CALLING ( ch_sorted_bam, ch_sorted_bai, ch_fasta, ch_fai )
+            ch_software_versions = ch_software_versions.mix(STRUCTURAL_VARIANT_CALLING.out.ch_versions.first().ifEmpty(null))
+        }
+    }
+
     ch_featurecounts_gene_multiqc       = Channel.empty()
     ch_featurecounts_transcript_multiqc = Channel.empty()
     if (!params.skip_quantification && (params.protocol == 'cDNA' || params.protocol == 'directRNA')) {