add sortgff and gff3trimfasta modules

modules/ebi-metagenomics/gff3trimfasta/main.nf

@@ -0,0 +1,39 @@
+process GFF3_TRIM_FASTA {
+    tag "$meta.id"
+    label 'process_single'
+
+    container 'quay.io/biocontainers/gawk:4.1.3--0'
+
+    input:
+    tuple val(meta), path(tab)
+
+    output:
+    tuple val(meta), path("*._trimmed.gff"), optional: true, emit: gff
+    path  "versions.yml"                                   , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    """
+
+    awk '/##FASTA/{exit}1' "$tab" > "${prefix}_trimmed.gff"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        awk: \$(awk --version 2>&1 | grep -o '[0-9]\{8\}')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch "${prefix}_trimmed.gff"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        awk: \$(awk --version 2>&1 | grep -o '[0-9]\{8\}')
+    END_VERSIONS
+    """
+}

modules/ebi-metagenomics/gff3trimfasta/meta.yml

@@ -0,0 +1,48 @@
+name: gff3trimfasta
+description: Trim the FASTA section from a GFF3 file
+keywords:
+  - trim
+  - gff
+  - fasta
+  - awk
+tools:
+  - awk:
+      description: A program that you can use to select particular records in a file and perform operations upon them.
+      homepage: https://www.gnu.org/software/gawk/
+      documentation: https://www.gnu.org/software/gawk/manual/gawk.html
+      licence: ["GPL-3.0-or-later"]
+      identifier: biotools:awk
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - tab:
+        type: file
+        description: |
+          GFF3 file that includes a FASTA section to be trimmed
+        pattern: "*.{gff,gff3}"
+output:
+  - gff:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_trimmed.gff":
+          type: file
+          description: GFF file with the FASTA section trimmed
+          pattern: "*_trimmed.gff"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@SantiagoSanchezF"
+  - "@tgurbich"
+  - "@vikasguptaebi"
+maintainers:
+  - "@tgurbich"
+  - "@vikasguptaebi"

modules/ebi-metagenomics/jbrowse/sortgff/main.nf

@@ -0,0 +1,40 @@
+process SORT_GFF {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container 'quay.io/biocontainers/coreutils:8.25--0'
+
+    input:
+    tuple val(meta), path(tab)
+
+    output:
+    tuple val(meta), path("*._sorted.gff"), optional:true, emit: gff
+    path  "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
+
+    """
+    (grep "^#" $tab; grep -v "^#" $tab | sort -t"`printf '\t'`" -k1,1 -k4,4n)  > ${prefix}.sorted.gff;
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        grep: \$(grep --version| awk '{print $NF}')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch ${prefix}.sorted.gff
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        grep: \$(grep --version| awk '{print $NF}')
+    END_VERSIONS
+    """
+}

modules/ebi-metagenomics/jbrowse/sortgff/meta.yml

@@ -0,0 +1,54 @@
+name: sortgff
+description: sort gff file for jbrowse use
+keywords:
+  - gff
+  - jbrowse
+  - sort
+  - grep
+tools:
+  - grep:
+      description: Print lines matching a pattern
+      homepage: https://www.gnu.org/software/grep/
+      documentation: https://www.gnu.org/software/grep/manual/
+      licence: ["GPL-3.0-or-later"]
+      identifier: biotools:grep
+  - sort:
+      description: Sort lines of text files
+      homepage: https://www.gnu.org/software/coreutils/
+      documentation: https://www.gnu.org/software/coreutils/manual/html_node/sort-invocation.html
+      licence: ["GPL-3.0-or-later"]
+      identifier: biotools:sort
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - tab:
+        type: file
+        description: |
+          GFF file containig genomic annotations
+        pattern: "*.{gff,gff3}"
+output:
+  - gff:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.sorted.gff":
+          type: file
+          description: Sorted GFF file
+          pattern: "*.sorted.gff"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@SantiagoSanchezF"
+  - "@tgurbich"
+  - "@vikasguptaebi"
+maintainers:
+  - "@tgurbich"
+  - "@vikasguptaebi"