Merge branch 'dev' into dev

.gitignore

@@ -9,4 +9,4 @@ results/
 test.xml
 testing*
 testing/
-work/
+work/

bin/busco_2_table.py

@@ -1,3 +1,4 @@
+#!/usr/bin/python3
 import pandas as pd
 import argparse
 

bin/plot_tree_summary.R

@@ -1,3 +1,4 @@
+#!/usr/bin/Rscript
 # Load necessary libraries
 if (!requireNamespace("argparse", quietly = TRUE)) {
   install.packages("argparse")

bin/plot_tree_summary2.R

@@ -1,3 +1,4 @@
+#!/usr/bin/Rscript
 # Load necessary libraries
 if (!requireNamespace("argparse", quietly = TRUE)) {
   install.packages("argparse")

bin/quast_2_table.py

@@ -1,3 +1,4 @@
+#!/usr/bin/python3
 import pandas as pd
 import argparse
 import os

conf/modules.config

@@ -95,4 +95,11 @@ process {
         ]
     }
 
+    withName: 'LONGEST' {
+        publishDir = [
+            path: { "$params.outdir/output_data/longest" }, 
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 }

conf/test_full.config

@@ -12,7 +12,7 @@
 
 params {
     config_profile_name        = 'Full test profile'
-    config_profile_description = 'Full test dataset of hymenpotera genomes'
+    config_profile_description = 'Full test dataset of Hymenoptera genomes'
 
     input = 'assets/samplesheet.csv'
 

modules.json

@@ -5,6 +5,11 @@
     "https://github.com/nf-core/modules.git": {
       "modules": {
         "nf-core": {
+          "agat/convertspgxf2gxf": {
+            "branch": "master",
+            "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+            "installed_by": ["modules"]
+          },
           "agat/spstatistics": {
             "branch": "master",
             "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",

modules/local/gffread.nf

@@ -63,9 +63,9 @@ process GFFREAD {
 
     fi
 
-    ${projectDir}/bin/gff_to_genetranshash.2.pl
-    ${projectDir}/bin/prot_fasta_to_longest.pl ${prefix}.prot.fa ${prefix}_longestisoform.txt
-    ${projectDir}/bin/fasta_topIsoform.pl ${prefix}.splicedcds.fa ${prefix}_longestisoform.txt
+    gff_to_genetranshash.2.pl
+    prot_fasta_to_longest.pl ${prefix}.prot.fa ${prefix}_longestisoform.txt
+    fasta_topIsoform.pl ${prefix}.splicedcds.fa ${prefix}_longestisoform.txt
 
 
     #This part checks if longest isoform worked, if not we will continue with all proteins into Orthofinder. Warning sent to screen.

modules/local/longest.nf

@@ -4,7 +4,6 @@ process LONGEST {
     label 'process_med_memory'
 
     container = 'biocontainers/agat:1.3.0--pl5321hdfd78af_0'
-    publishDir "$params.outdir/output_data/longest" , mode: "${params.publish_dir_mode}", pattern:"*.txt"
 
     input:
     tuple val (meta),  path(gff)

modules/local/tree_summary.nf

@@ -27,18 +27,18 @@ process TREE_SUMMARY {
     cut -f 1,3,4,5,6,7 Busco_combined >> Busco_combined_cut
     sed -i \'s/\\.fasta//g\' Busco_combined_cut
 
-    python3 ${projectDir}/bin/busco_2_table.py Busco_combined_cut Busco_to_plot.tsv
+    busco_2_table.py Busco_combined_cut Busco_to_plot.tsv
 
     # Combine QUAST ouput
-    python3 ${projectDir}/bin/quast_2_table.py *quast.tsv -o Quast_to_plot.tsv -col N50,N90 -plot_types bar,bar
+    quast_2_table.py *quast.tsv -o Quast_to_plot.tsv -col N50,N90 -plot_types bar,bar
 
     #Remove unwanted extensions from Busco tables
     sed \'s/.prot.fa.largestIsoform.fa//g\' Busco_to_plot.tsv > Busco_to_plot_final.tsv
     sed \'s/.prot.fa.largestIsoform.fa//g\' Quast_to_plot.tsv > Quast_to_plot_final.tsv
 
     # Run summary plot
-    /usr/bin/Rscript ${projectDir}/bin/plot_tree_summary2.R tree.nw Busco_to_plot_final.tsv --tree_size 0.6
-    /usr/bin/Rscript ${projectDir}/bin/plot_tree_summary.R  tree.nw Quast_to_plot_final.tsv --tree_size 0.6
+    plot_tree_summary2.R tree.nw Busco_to_plot_final.tsv --tree_size 0.6
+    plot_tree_summary.R  tree.nw Quast_to_plot_final.tsv --tree_size 0.6
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/agat/convertspgxf2gxf/environment.yml

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::agat=1.4.0

modules/nf-core/agat/convertspgxf2gxf/main.nf

@@ -0,0 +1,48 @@
+process AGAT_CONVERTSPGXF2GXF {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/agat:1.4.0--pl5321hdfd78af_0' :
+        'biocontainers/agat:1.4.0--pl5321hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(gxf)
+
+    output:
+    tuple val(meta), path("*.agat.gff") , emit: output_gff
+    tuple val(meta), path("*.log")      , emit: log
+    path "versions.yml"                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    agat_convert_sp_gxf2gxf.pl \\
+        --gxf $gxf \\
+        --output ${prefix}.agat.gff \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        agat: \$(agat_convert_sp_gxf2gxf.pl --help | sed -n 's/.*(AGAT) - Version: \\(.*\\) .*/\\1/p')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.agat.gff
+    touch ${gxf}.agat.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        agat: \$(agat_convert_sp_gxf2gxf.pl --help | sed -n 's/.*(AGAT) - Version: \\(.*\\) .*/\\1/p')
+    END_VERSIONS
+    """
+}

modules/nf-core/agat/convertspgxf2gxf/meta.yml

@@ -0,0 +1,56 @@
+name: agat_convertspgxf2gxf
+description: |
+  Fixes and standardizes GFF/GTF files and outputs a cleaned GFF/GTF file
+keywords:
+  - genome
+  - gff
+  - gtf
+  - conversion
+tools:
+  - agat:
+      description: "AGAT is a toolkit for manipulation and getting information from
+        GFF/GTF files"
+      homepage: "https://github.com/NBISweden/AGAT"
+      documentation: "https://agat.readthedocs.io/"
+      tool_dev_url: "https://github.com/NBISweden/AGAT"
+      doi: "10.5281/zenodo.3552717"
+      licence: ["GPL v3"]
+      identifier: biotools:AGAT
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - gxf:
+        type: file
+        description: Annotation file in GFF3/GTF format
+        pattern: "*.{gff, gtf}"
+output:
+  - output_gff:
+      - meta:
+          type: file
+          description: Cleaned annotation file in GFF3 format
+          pattern: "*.{gff}"
+      - "*.agat.gff":
+          type: file
+          description: Cleaned annotation file in GFF3 format
+          pattern: "*.{gff}"
+  - log:
+      - meta:
+          type: file
+          description: Log file of the conversion process
+          pattern: "*.{log}"
+      - "*.log":
+          type: file
+          description: Log file of the conversion process
+          pattern: "*.{log}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@toniher"
+maintainers:
+  - "@toniher"

modules/nf-core/agat/convertspgxf2gxf/tests/main.nf.test

@@ -0,0 +1,60 @@
+nextflow_process {
+
+    name "Test Process AGAT_CONVERTSPGXF2GXF"
+    script "../main.nf"
+    process "AGAT_CONVERTSPGXF2GXF"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "agat"
+    tag "agat/convertspgxf2gxf"
+
+    test("sarscov2 genome [gtf]") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id: 'test' ], // meta map
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.output_gff,
+                                process.out.versions).match() },
+                { assert path(process.out.log[0][1]).exists() }
+            )
+        }
+
+    }
+
+    test("sarscov2 genome [gtf] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id: 'test' ], // meta map
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/agat/convertspgxf2gxf/tests/main.nf.test.snap

@@ -0,0 +1,71 @@
+{
+    "sarscov2 genome [gtf] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.agat.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.gtf.agat.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,5ec6166c5c080ec4bc08a8fe55ada486"
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.gtf.agat.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "output_gff": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.agat.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5ec6166c5c080ec4bc08a8fe55ada486"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-12T12:25:34.583294"
+    },
+    "sarscov2 genome [gtf]": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.agat.gff:md5,7d7e9bcd82a2f0bb7d8a38f85e82f0bc"
+                ]
+            ],
+            [
+                "versions.yml:md5,5ec6166c5c080ec4bc08a8fe55ada486"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-12T12:21:21.310464"
+    }
+}

modules/nf-core/agat/convertspgxf2gxf/tests/tags.yml

@@ -0,0 +1,2 @@
+agat/convertspgxf2gxf:
+  - "modules/nf-core/agat/convertspgxf2gxf/**"