Long due nextflowmodules update

AGAT/0.8.1/ConvertGffToGtf.nf

@@ -0,0 +1,18 @@
+process ConvertGffToGtf {
+    tag {"AGAT ConvertGffToGtf ${gff}"}
+    label 'AGAT_0_8_1'
+    label 'AGAT_0_8_1_ConvertGffToGtf'
+    container = 'quay.io/biocontainers/agat:0.8.1--pl5262hdfd78af_0'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        path(gff)
+
+    output:
+        path("${gff.simpleName}.gtf", emit: gtf)
+
+    script:
+        """
+        agat_convert_sp_gff2gtf.pl -gff ${gff} -o ${gff.simpleName}.gtf
+        """
+}

BCFtools/1.10.2/View.nf

@@ -7,13 +7,13 @@ process View_bcf_vcf {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-    tuple(val(sample_id), file(bcf_file))
+        tuple(val(sample_id), file(bcf_file))
 
     output:
-    tuple(val(sample_id), file("${bcf_file.baseName}.vcf"))
+        tuple(val(sample_id), file("${bcf_file.baseName}.vcf"))
 
     script:
-    """
-    bcftools view ${params.optional} ${bcf_file} > ${bcf_file.baseName}.vcf
-    """
+        """
+        bcftools view ${params.optional} ${bcf_file} > ${bcf_file.baseName}.vcf
+        """
 }

BCFtools/1.17/View.nf

@@ -0,0 +1,20 @@
+process View_bcf_vcf {
+    // BCFtools view can use different input and output files, this process converts bcf to vcf files.
+    tag {"BCFtools View_BCF_VCF ${sample_id}"}
+    label 'BCFtools_1_17'
+    label 'BCFtools_1_17_View_BCF_VCF'
+    container = 'quay.io/biocontainers/bcftools:1.17--h3cc50cf_1'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        tuple(val(sample_id), file(input_file))
+
+    output:
+        tuple(val(sample_id), file("${input_file.baseName}.${extension}"))
+
+    script:
+        extension = input_file.getExtension() == "vcf" ? "bcf" : "vcf"
+        """
+        bcftools view ${params.optional} ${input_file} > ${input_file.baseName}.${extension}
+        """
+}

BWA-Mem2/bwa-mem2_samtools-1.12_2.2.1/BWASW.nf

@@ -0,0 +1,18 @@
+process BWASW {
+    tag {"BWA_MEM2 BWASW ${sample_id} - ${rg_id}"}
+    label 'BWA_MEM2_2_2_1'
+    label 'BWA_MEM2_2_2_1_BWASW'
+    container = 'blcdsdockerregistry/bwa-mem2_samtools-1.12:2.2.1'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        tuple(val(sample_id), val(rg_id), path(fastq))
+
+    output:
+        tuple(val(sample_id), val(rg_id_), path("${fastq[0].simpleName}.sam"), emit: sam_file)
+
+    script:
+        """
+        bwa-mem2 bwasw -t ${task.cpus} ${params.optional} ${params.genome} ${fastq} > ${fastq[0].simpleName}.sam
+        """
+}

BWA-Mem2/bwa-mem2_samtools-1.12_2.2.1/Index.nf

@@ -0,0 +1,22 @@
+index_loc = file("${params.genome_fasta}").toRealPath().toString().split("/")[0..-2].join("/")
+
+process Index {
+    tag {"BWA_MEM2 Index $fasta"}
+    label 'BWA_MEM2_2_2_1'
+    label 'BWA_MEM2_2_2_1_Index'
+    container = 'library://blcdsdockerregistry/bwa-mem2_samtools-1.12:2.2.1'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    storeDir = index_loc
+
+    input:
+        path(fasta)
+
+    output:
+        path("${fasta}.{alt,amb,ann,bwt,pac,sa}", emit: bwa_index)
+
+    script:
+        """
+        bwa-mem2 index $params.optional $fasta
+        """
+}

BWA-Mem2/bwa-mem2_samtools-1.12_2.2.1/MEM.nf

@@ -0,0 +1,21 @@
+process MEM {
+    tag {"BWA_MEM2 MEM ${sample_id} - ${rg_id}"}
+    label 'BWA_MEM2_2_2_1'
+    label 'BWA_MEM2_2_2_1_MEM'
+    container = 'quay.io/blcdsdockerregistry/bwa-mem2_samtools-1.12:2.2.1'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        tuple(val(sample_id), val(rg_id), path(fastq))
+
+    output:
+        tuple(val(sample_id), val(rg_id), path("${fastq[0].simpleName}.sam"), emit: sam_file)
+
+    script:
+        def barcode = rg_id.split('_')[1]
+        def readgroup = "\"@RG\\tID:${rg_id}\\tSM:${sample_id}\\tPL:ILLUMINA\\tLB:${sample_id}\\tPU:${barcode}\""
+
+        """
+        bwa-mem2 mem -t ${task.cpus} -R ${readgroup} ${params.optional} ${params.genome} ${fastq} > ${fastq[0].simpleName}.sam
+        """
+}

BWA-Mem2/bwa-mem2_samtools-1.12_2.2.1/Mapping.nf

@@ -0,0 +1,23 @@
+process BWAMapping {
+    tag {"BWA_MEM2 Mem ${sample_id} - ${rg_id}"}
+    label 'BWA_MEM2_2_2_1'
+    label 'BWA_MEM2_2_2_1_Mem'
+    container = 'library://blcdsdockerregistry/bwa-mem2_samtools-1.12:2.2.1'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        tuple(val(sample_id), val(rg_id), path(fastq))
+
+    output:
+        tuple(val(sample_id), val(rg_id), path("${rg_id}_sorted.bam"), path("${rg_id}_sorted.bai"), emit: mapped_bams)
+
+    script:
+        def barcode = rg_id.split('_')[1]
+        def bwa_readgroup = "\"@RG\\tID:${rg_id}\\tSM:${sample_id}\\tPL:ILLUMINA\\tLB:${sample_id}\\tPU:${barcode}\""
+
+        """
+        bwa-mem2 mem $params.optional -t ${task.cpus} -R $bwa_readgroup $params.genome_fasta $fastq | \
+        samtools sort > ${rg_id}_sorted.bam
+        samtools index ${rg_id}_sorted.bam ${rg_id}_sorted.bai
+        """
+}

ControlFREEC/11.6/AssessSignificance.nf

@@ -0,0 +1,18 @@
+process AssessSignificance {
+    tag {"Control Freec AssessSignificance ${sample_id}"}
+    label 'ControlFreec_11_6'
+    label 'ControlFreec_11_6_AssessSignificance'
+    container = 'quay.io/biocontainers/control-freec:11.6--h87f3376_2'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        tuple(val(sample_id), path(ratio_file), path(cnv_file))
+
+    output:
+        tuple(val(sample_id), path("${cnv_file.name}.p.value.txt"), emit: cnv_pvalue)
+
+    script:
+        """
+        cat /usr/local/bin/assess_significance.R | R --slave --args ${cnv_file} ${ratio_file}
+        """
+}

ControlFREEC/11.6/Freec.nf

@@ -0,0 +1,35 @@
+process Freec {
+    tag {"Control Freec ${sample_id}"}
+    label 'ControlFreec_11_6'
+    label 'ControlFreec_11_6_Freec'
+    container = 'quay.io/biocontainers/control-freec:11.6--h87f3376_2'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        tuple(val(sample_id), path(bam_file), path(bai_file))
+
+    output:
+        tuple(val(sample_id), path("${bam_file.name}_ratio.txt"), path("${bam_file.name}_CNVs"), emit: cnv)
+        tuple(val(sample_id), path("${bam_file.name}_sample.cpn"), path("${bam_file.name}_ratio.BedGraph"), path("${bam_file.name}_info.txt"), emit: other)
+
+    script:
+        def config = "${sample_id}.config"
+        """
+        touch ${config}
+        echo "[general]" >> ${config}
+        echo "chrLenFile = ${params.chr_len_file}" >> ${config}
+        echo "chrFiles = ${params.chr_files}" >> ${config}
+        echo "gemMappabilityFile = ${params.gem_mappability_file}" >> ${config}
+        echo "ploidy = ${params.ploidy}" >> ${config}
+        echo "window = ${params.window}" >> ${config}
+        echo "telocentromeric = ${params.telocentromeric}" >> ${config}
+        echo "BedGraphOutput=TRUE" >> ${config}
+        echo "maxThreads=${task.cpus}" >> ${config}
+
+        echo "[sample]" >> ${config}
+        echo "inputFormat = BAM" >> ${config}
+        echo "mateFile = ${bam_file}" >> ${config}
+
+        freec -conf ${config}
+        """
+}

ControlFREEC/11.6/MakeGraph.nf

@@ -0,0 +1,18 @@
+process MakeGraph {
+    tag {"Control Freec MakeGraph ${sample_id}"}
+    label 'ControlFreec_11_6'
+    label 'ControlFreec_11_6_MakeGraph'
+    container = 'quay.io/biocontainers/control-freec:11.6--h87f3376_2'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        tuple(val(sample_id), path(ratio_file), path(cnv_file))
+
+    output:
+        tuple(val(sample_id), path("${ratio_file.name}.png"), path("${ratio_file.name}.log2.png"), emit: ratio_png)
+
+    script:
+        """
+        cat /usr/local/bin/makeGraph.R | R --slave --args ${params.ploidy} ${ratio_file}
+        """
+}

ControlFREEC/11.6/MakeGraphChromosome.nf

@@ -0,0 +1,18 @@
+process MakeGraphChromosome {
+    tag {"Control Freec MakeGraphChromosome ${sample_id}"}
+    label 'ControlFreec_11_6'
+    label 'ControlFreec_11_6_MakeGraphChromosome'
+    container = 'quay.io/biocontainers/control-freec:11.6--h87f3376_2'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        tuple(val(sample_id), path(ratio_file), path(cnv_file))
+
+    output:
+        tuple(val(sample_id), path("${ratio_file.name}*.png"), emit: ratio_png)
+
+    script:
+        """
+        cat /usr/local/bin/makeGraph_Chromosome.R | R --slave --args 1 ${params.ploidy} ${ratio_file}
+        """
+}

ControlFREEC/11.6/MakeKaryotype.nf

@@ -0,0 +1,18 @@
+process MakeKaryotype {
+    tag {"Control Freec MakeKaryotype ${sample_id}"}
+    label 'ControlFreec_11_6'
+    label 'ControlFreec_11_6_MakeKaryotype'
+    container = 'quay.io/biocontainers/control-freec:11.6--h87f3376_2'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        tuple(val(sample_id), path(ratio_file), path(cnv_file))
+
+    output:
+        tuple(val(sample_id), path("*_karyotype.pdf"), emit: karyotype_pdf)
+
+    script:
+        """
+        cat makeKaryotype.R | R --slave --args ${params.ploidy} ${params.maxlevel} ${params.telocentromeric} ${ratio_file}
+        """
+}

DESeq2/1.28.0/deseq2Normalize.nf

@@ -0,0 +1,20 @@
+process Deseq2Normalize {
+    tag "deseq2normalize ${run_id}"
+    label 'biconductor_1_28_0'
+    label 'biconductor_1_28_0_deseq2normalize'
+    container = 'quay.io/biocontainers/bioconductor-deseq2:1.28.0--r40h5f743cb_0'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        val(run_id)
+        file(counts)
+
+    output:
+        file("${run_id}_featureCounts_deseq2.txt")
+
+    script:
+        """
+        deseq2Normalize.R ${counts} ${run_id}  
+        """
+
+}

DESeq2/1.38.0/deseq2Normalize.nf

@@ -0,0 +1,19 @@
+process Deseq2Normalize {
+    tag "deseq2normalize ${run_id}"
+    label 'biconductor_1_38_0'
+    label 'biconductor_1_38_0_deseq2normalize'
+    container = 'quay.io/biocontainers/bioconductor-deseq2:1.38.0--r42hc247a5b_0'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        val(run_id)
+        file(counts)
+
+    output:
+        file("${run_id}_featureCounts_deseq2.txt")
+
+    script:
+        """
+        deseq2Normalize.R ${counts} ${run_id}  
+        """
+}

Deeplexicon/1.2.0/dmux.nf

@@ -0,0 +1,25 @@
+process dmux {
+    tag {"Deeplexicon_dmux"}
+    label 'Deeplexicon_1_2_0'
+    label 'Deeplexicon_1_2_0_dmux'
+    container = 'lpryszcz/deeplexicon:1.2.0'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        tuple(val(sample), val(chunk), path(fast5))
+
+    output:
+        tuple(val(sample), val(chunk), path("${sample}_${chunk}.demux2.tsv"), emit:tsv)
+
+    script:
+        """
+        #deeplexicon only works when folder is passed, not when fast5 itself is used so put file in folder for further processing
+        mkdir fast5_folder
+        cp -P ${fast5} fast5_folder/
+        deeplexicon_multi.py dmux \
+	    --threads 2 \
+            -p ./fast5_folder/ \
+            -m /deeplexicon/models/resnet20-final.h5 \
+        > ${sample}_${chunk}.demux2.tsv
+        """
+}

Deeplexicon/1.2.0/fastq.nf

@@ -0,0 +1,18 @@
+process deeplexicon_concatFastq {
+    tag {"Deeplexicon_concat_fastq"}
+    label 'Deeplexicon_1_2_0'
+    label 'Deeplexicon_1_2_0_concat_fastq'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        tuple(val(id), val(chunk), path(fastq))
+
+    output:
+	tuple(val(id), path("${id}_combined.fastq"), emit:fastq)
+
+    script:
+        """
+        cat *.fastq.gz > ${id}_combined.fastq.gz
+        gunzip ${id}_combined.fastq.gz
+        """
+}

Deeplexicon/1.2.0/split.nf

@@ -0,0 +1,25 @@
+process split {
+    tag {"Deeplexicon_split"}
+    label 'Deeplexicon_1_2_0'
+    label 'Deeplexicon_1_2_0_split'
+    container = 'lpryszcz/deeplexicon:1.2.0'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        tuple(val(id), path(tsv),path(fastq))
+
+    output:
+        path("*.fastq.gz")
+
+    script:
+        """
+        deeplexicon_multi.py split \
+            -i ${tsv} \
+            -o . \
+            -s ${id} \
+            -q ${fastq}
+
+        #deeplexicon outputs plain fastq, so gzip them
+        gzip ${id}_bc_*.fastq
+        """
+}