Huge effort to finally update modules done :)

modules/local/gatk4/filtersamreads/main.nf

@@ -0,0 +1,39 @@
+process GATK4_FILTERSAMREADS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(read_ids)
+    val fasta  // treat it as a string because FilterSamReads is unable to solve softlinking
+
+    output:
+    tuple val(meta), path("*.bam"), path("*.bai") , emit: bam
+    path "versions.yml"                           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def fastastr = fasta[0].toString()
+
+    """
+    gatk FilterSamReads \\
+       --INPUT $bam \\
+       --OUTPUT ${prefix}.bam \\
+       --TMP_DIR . \\
+       -R ${fastastr} \\
+       $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/local/gatk4/filtersamreads/meta.yml

@@ -0,0 +1,50 @@
+name: gatk4_filtersamreads
+description: |
+  Subsets reads from a SAM or BAM file by applying one of several filters.
+keywords:
+  - gatk4
+  - reads
+  - BAM
+  - SAM
+tools:
+  - gatk4:
+      description: |
+        Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
+        with a primary focus on variant discovery and genotyping. Its powerful processing engine
+        and high-performance computing features make it capable of taking on projects of any size.
+      homepage: https://gatk.broadinstitute.org/hc/en-us
+      documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
+      doi: 10.1158/1538-7445.AM2017-3590
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - bam:
+      type: file
+      description: compressed vcf file of mutect2calls
+      pattern: "*.bam"
+  - read_ids:
+      type: file
+      description: File with read ids to keep
+      pattern: "*.txt"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - bam:
+      type: file
+      description: compressed vcf file of mutect2calls
+      pattern: "*.bam"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@RaqManzano"

modules/local/sage/main.nf

@@ -0,0 +1,92 @@
+def VERSION = '3.1'  // Version information not provided by tool on CLI
+
+process SAGE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::hmftools-sage=3.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hmftools-sage:3.1--hdfd78af_0' :
+        'quay.io/biocontainers/hmftools-sage:3.1--hdfd78af_0' }"
+
+    input:
+        tuple val(meta), path(normal), path(normal_index), path(tumor), path(tumor_index), path(intervals)
+        path fasta
+        path fasta_fai
+        path dict
+        path highconfidence
+        path actionablepanel
+        path knownhot
+        path ensbl_sage
+
+    output:
+        tuple val(meta), path("*.vcf"), emit: vcf
+        path  "versions.yml"          , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args = task.ext.args ?: ''
+        def prefix = task.ext.prefix ?: "${meta.id}"
+        def reference             = normal          ? "-reference ${meta.normal_id} -reference_bam ${normal}" : ""
+        def HighConfidence        = highconfidence  ? "-high_confidence_bed ${highconfidence}"                : ""
+        def ActionableCodingPanel = actionablepanel ? "-panel_bed ${actionablepanel}"                         : ""
+        def KnownHotspots         = knownhot        ? "-hotspots ${knownhot}"                                 : ""
+        def avail_mem = 4
+        if (!task.memory) {
+            log.info '[SAGE] Available memory not known - defaulting to 4GB. Specify process memory requirements to change this.'
+        } else {
+            avail_mem = task.memory.giga
+        }
+        if (intervals){ // If no reads the intervals don't work in sage
+        """
+        export _JAVA_OPTIONS="-Xmx${avail_mem}g"
+        INTER=\$(sed -E 's/\\s+0\\s+/\\t1\\t/g' $intervals | grep -v chrM | sed 's/\t/:/g' | paste -s -d ';')
+
+        SAGE \\
+            -out ${prefix}.vcf \\
+            -ref_genome $fasta \\
+            -threads $task.cpus \\
+            -tumor ${meta.tumor_id} \\
+            -tumor_bam ${tumor} \\
+            $reference \\
+            -ensembl_data_dir $ensbl_sage \\
+            $HighConfidence \\
+            $ActionableCodingPanel \\
+            $KnownHotspots \\
+            -specific_regions \$INTER \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            sage: $VERSION
+        END_VERSIONS
+        """
+
+        } else {
+        """
+        export _JAVA_OPTIONS="-Xmx${avail_mem}g"
+        SAGE \\
+            -out ${prefix}.vcf \\
+            -ref_genome $fasta \\
+            -threads $task.cpus \\
+            -tumor ${meta.tumor_id} \\
+            -tumor_bam ${tumor} \\
+            $reference \\
+            -ensembl_data_dir $ensbl_sage \\
+            $HighConfidence \\
+            $ActionableCodingPanel \\
+            $KnownHotspots \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            sage: $VERSION
+        END_VERSIONS
+        """
+        }
+
+
+
+}

modules/local/sage/meta.yml

@@ -0,0 +1,77 @@
+name: sage
+description: SAGE is a precise and highly sensitive somatic SNV, MNV and small INDEL caller. It has been optimised for 100x tumor / 40x normal coverage, but has a flexible set of filters that can be adapted to lower or higher depth coverage.
+keywords:
+  - variant caller
+  - SNP
+  - indels
+  - somatic variant calling
+  - hmftools
+
+tools:
+  - sage:
+      description: SAGE is a precise and highly sensitive somatic SNV, MNV and small INDEL caller.
+      homepage: https://github.com/hartwigmedical/hmftools/blob/master/sage/README.md
+      documentation: https://github.com/hartwigmedical/hmftools/tree/master/sage
+      tool_dev_url: https://github.com/hartwigmedical/hmftools/tree/master/sage
+      licence: ["GPL-3.0"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - normal:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - normal_index:
+      type: file
+      description: BAM/CRAM/SAM index file
+      pattern: "*.{bai,crai}"
+  - tumor:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - tumor_index:
+      type: file
+      description: BAM/CRAM/SAM index file
+      pattern: "*.{bai,crai}"
+  - intervals:
+      type: file
+      description: BED file for intervals
+      pattern: "*.bed"
+  - fasta:
+      type: file
+      description: reference fasta file
+      pattern: ".{fa,fa.gz,fasta,fasta.gz}"
+  - highconfidence:
+      type: file
+      description: Optional.
+      pattern: "*.bed"
+  - actionablepanel:
+      type: file
+      description: Optional.
+      pattern: "*.bed"
+  - knownhot:
+      type: file
+      description: Optional.
+      pattern: "*.bed"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: Compressed VCF file
+      pattern: "*.vcf.gz"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+
+authors:
+  - "@RaqManzano"

modules/local/vcflib/filter/main.nf

@@ -0,0 +1,34 @@
+process VCFFILTER {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::vcftools=0.1.16" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/vcflib:1.0.3--hecb563c_1' :
+        'quay.io/biocontainers/vcflib:1.0.3--hecb563c_1' }"
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta), path("*.vcf.gz")                    , emit: vcf
+    path "versions.yml"                               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+
+    gunzip -c $vcf | vcffilter \\
+        $args > ${prefix}.vcf
+    gzip ${prefix}.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vcffilter: \$(echo \$(vcffilter 2>&1) | sed 's/^.*vcflib ( //;s/).*//' | cut -f2 -d ' ')
+    END_VERSIONS
+    """
+}

modules/local/vcflib/filter/meta.yml

@@ -0,0 +1,45 @@
+name: vcffilter
+description: VCF filter the specified vcf file using the set of filters
+
+keywords:
+  - VCF
+  - filter
+  - variant calling
+tools:
+  - vcffilter:
+      description: VCF filter the specified vcf file using the set of filters
+      homepage: https://github.com/vcflib/vcflib
+      documentation: https://github.com/vcflib/vcflib
+      tool_dev_url: https://github.com/vcflib/vcflib
+      doi:  https://doi.org/10.1101/2021.05.21.445151
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: vcf file (optional)
+      pattern: "*.vcf.gz"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - vcf:
+      type: file
+      description: vcf file (optional)
+      pattern: "*.vcf.gz"
+
+
+authors:
+  - "@RaqManzano"