Merge branch 'master' into tool/elprep-merge

2024-12-22 11:08:17 +00:00 · 2022-04-24 10:08:29 +02:00 · 2022-04-24 10:08:29 +02:00 · 978f665c0a
commit 978f665c0a
parent 9a2dad935c 378fa5fbb4
18 changed files with 177 additions and 35 deletions
--- a/modules/cat/fastq/main.nf
+++ b/modules/cat/fastq/main.nf
@ -4,8 +4,8 @@ process CAT_FASTQ {

    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
-        'biocontainers/biocontainers:v1.2.0_cv1' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"

    input:
    tuple val(meta), path(reads, stageAs: "input*/*")
--- a/modules/gamma/main.nf
+++ b/modules/gamma/main.nf
@ -0,0 +1,41 @@
+def VERSION = '2.1' // Version information not provided by tool on CLI
+
+process GAMMA {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::gamma=2.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gamma%3A2.1--hdfd78af_0':
+        'quay.io/biocontainers/gamma:2.1--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+    path(db)
+
+    output:
+    tuple val(meta), path("*.gamma")                , emit: gamma
+    tuple val(meta), path("*.psl")                  , emit: psl
+    tuple val(meta), path("*.gff")  , optional:true , emit: gff
+    tuple val(meta), path("*.fasta"), optional:true , emit: fasta
+    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}"
+    """
+    GAMMA.py \\
+        $args \\
+        $fasta \\
+        $db \\
+        $prefix
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gamma: $VERSION
+    END_VERSIONS
+    """
+}
--- a/modules/gamma/meta.yml
+++ b/modules/gamma/meta.yml
@ -0,0 +1,63 @@
+name: "gamma"
+description: Gene Allele Mutation Microbial Assessment
+keywords:
+  - gamma
+  - gene-calling
+tools:
+  - "gamma":
+      description: "Tool for Gene Allele Mutation Microbial Assessment"
+      homepage: "https://github.com/rastanton/GAMMA"
+      documentation: "https://github.com/rastanton/GAMMA"
+      tool_dev_url: "https://github.com/rastanton/GAMMA"
+      doi: "10.1093/bioinformatics/btab607"
+      licence: "['Apache License 2.0']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: FASTA file
+      pattern: "*.{fa,fasta}"
+  - db:
+      type: file
+      description: Database in FASTA format
+      pattern: "*.{fa,fasta}"
+
+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"
+
+  - gamma:
+      type: file
+      description: GAMMA file with annotated gene matches
+      pattern: "*.{gamma}"
+
+  - psl:
+      type: file
+      description: PSL file with all gene matches found
+      pattern: "*.{psl}"
+
+  - gff:
+      type: file
+      description: GFF file
+      pattern: "*.{gff}"
+
+  - fasta:
+      type: file
+      description: multifasta file of the gene matches
+      pattern: "*.{fasta}"
+
+authors:
+  - "@sateeshperi"
+  - "@rastanton"
--- a/modules/gunzip/main.nf
+++ b/modules/gunzip/main.nf
@ -4,8 +4,8 @@ process GUNZIP {

    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
-        'biocontainers/biocontainers:v1.2.0_cv1' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"

    input:
    tuple val(meta), path(archive)
--- a/modules/phantompeakqualtools/main.nf
+++ b/modules/phantompeakqualtools/main.nf
@ -26,7 +26,7 @@ process PHANTOMPEAKQUALTOOLS {
    def prefix = task.ext.prefix ?: "${meta.id}"
    """
    RUN_SPP=`which run_spp.R`
-    Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus
+    Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out"

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
--- a/modules/stringtie/merge/main.nf
+++ b/modules/stringtie/merge/main.nf
@ -2,10 +2,10 @@ process STRINGTIE_MERGE {
    label 'process_medium'

    // Note: 2.7X indices incompatible with AWS iGenomes.
-    conda     (params.enable_conda ? "bioconda::stringtie=2.1.7" : null)
+    conda     (params.enable_conda ? "bioconda::stringtie=2.2.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0' :
-        'quay.io/biocontainers/stringtie:2.1.7--h978d192_0' }"
+        'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
+        'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }"

    input:
    path stringtie_gtf
--- a/modules/stringtie/stringtie/main.nf
+++ b/modules/stringtie/stringtie/main.nf
@ -1,11 +1,11 @@
-process STRINGTIE {
+process STRINGTIE_STRINGTIE {
    tag "$meta.id"
    label 'process_medium'

-    conda (params.enable_conda ? "bioconda::stringtie=2.1.7" : null)
+    conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0' :
-        'quay.io/biocontainers/stringtie:2.1.7--h978d192_0' }"
+        'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
+        'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }"

    input:
    tuple val(meta), path(bam)
--- a/modules/stringtie/stringtie/meta.yml
+++ b/modules/stringtie/stringtie/meta.yml
@ -1,4 +1,4 @@
-name: stringtie
+name: stringtie_stringtie
 description: Transcript assembly and quantification for RNA-Se
 keywords:
  - transcript
--- a/modules/untar/main.nf
+++ b/modules/untar/main.nf
@ -2,10 +2,10 @@ process UNTAR {
    tag "$archive"
    label 'process_low'

-    conda (params.enable_conda ? "conda-forge::tar=1.34" : null)
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
-        'biocontainers/biocontainers:v1.2.0_cv2' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"

    input:
    tuple val(meta), path(archive)
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@ -679,6 +679,10 @@ freebayes:
  - modules/freebayes/**
  - tests/modules/freebayes/**

+gamma:
+  - modules/gamma/**
+  - tests/modules/gamma/**
+
 gatk4/applybqsr:
  - modules/gatk4/applybqsr/**
  - tests/modules/gatk4/applybqsr/**
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@ -335,6 +335,7 @@ params {
        'bacteroides_fragilis' {
            'genome' {
                genome_fna_gz                   = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz"
+                genome_gbff_gz                  = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz"
                genome_paf                      = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf"
                genome_mapping_potential_arg    = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.mapping.potential.ARG"

--- a/tests/modules/gamma/main.nf
+++ b/tests/modules/gamma/main.nf
@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GAMMA } from '../../../modules/gamma/main.nf'
+
+workflow test_gamma {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    db = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+
+    GAMMA ( input, db )
+}
--- a/tests/modules/gamma/nextflow.config
+++ b/tests/modules/gamma/nextflow.config
@ -0,0 +1,7 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    ext.args = '--fasta'
+
+}
--- a/tests/modules/gamma/test.yml
+++ b/tests/modules/gamma/test.yml
@ -0,0 +1,13 @@
+- name: gamma test_gamma
+  command: nextflow run tests/modules/gamma -entry test_gamma -c tests/config/nextflow.config
+  tags:
+    - gamma
+  files:
+    - path: output/gamma/test.fasta
+      md5sum: df37b48466181311e0a679f3c5878484
+    - path: output/gamma/test.gamma
+      md5sum: 3256708fa517a65ed01d99e0e3c762ae
+    - path: output/gamma/test.psl
+      md5sum: 162a2757ed3b167ae1e0cdb24213f940
+    - path: output/gamma/versions.yml
+      md5sum: 3fefb5b46c94993362243c5f9a472057
--- a/tests/modules/stringtie/merge/main.nf
+++ b/tests/modules/stringtie/merge/main.nf
@ -2,8 +2,8 @@

 nextflow.enable.dsl = 2

-include { STRINGTIE       } from '../../../../modules/stringtie/stringtie/main.nf'
-include { STRINGTIE_MERGE } from '../../../../modules/stringtie/merge/main.nf'
+include { STRINGTIE_STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
+include { STRINGTIE_MERGE     } from '../../../../modules/stringtie/merge/main.nf'

 /*
 * Test with forward strandedness
@ -15,8 +15,8 @@ workflow test_stringtie_forward_merge {
    ]
    annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)

-    STRINGTIE ( input, annotation_gtf )
-    STRINGTIE
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
+    STRINGTIE_STRINGTIE
        .out
        .transcript_gtf
        .map { it -> it[1] }
@ -35,8 +35,8 @@ workflow test_stringtie_reverse_merge {
    ]
    annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)

-    STRINGTIE ( input, annotation_gtf )
-    STRINGTIE
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
+    STRINGTIE_STRINGTIE
        .out
        .transcript_gtf
        .map { it -> it[1] }
--- a/tests/modules/stringtie/merge/test.yml
+++ b/tests/modules/stringtie/merge/test.yml
@ -5,7 +5,7 @@
    - stringtie/merge
  files:
    - path: output/stringtie/stringtie.merged.gtf
-      md5sum: 9fab7049ef2eafdea246fc787d1def40
+      md5sum: d959eb2fab0db48ded7275e0a2e83c05
    - path: output/stringtie/test.ballgown/e2t.ctab
      md5sum: 9ae42e056c955a88a883e5e917840d77
    - path: output/stringtie/test.ballgown/e_data.ctab
@ -17,11 +17,10 @@
    - path: output/stringtie/test.ballgown/t_data.ctab
      md5sum: 92a98902784e7406ffe054d2adbabc7c
    - path: output/stringtie/test.coverage.gtf
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: output/stringtie/test.gene.abundance.txt
-      md5sum: 9708811bcefe0f6384293d6f419f3250
+      md5sum: 8bcd8e2730ed3337e2730186dbc184f3
    - path: output/stringtie/test.transcripts.gtf
-      md5sum: 0e42709bfe30c2c7f2574ba664f5fa9f
+      md5sum: a914bd55b68a4b5f607738b17861e362

 - name: stringtie merge test_stringtie_reverse_merge
  command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config
@ -30,7 +29,7 @@
    - stringtie/merge
  files:
    - path: output/stringtie/stringtie.merged.gtf
-      md5sum: afc461bb3cbc368f268a7a45c1b54497
+      md5sum: 6da479298d73d5b3216d4e1576a2bdf4
    - path: output/stringtie/test.ballgown/e2t.ctab
      md5sum: 9ae42e056c955a88a883e5e917840d77
    - path: output/stringtie/test.ballgown/e_data.ctab
@ -42,8 +41,7 @@
    - path: output/stringtie/test.ballgown/t_data.ctab
      md5sum: 92a98902784e7406ffe054d2adbabc7c
    - path: output/stringtie/test.coverage.gtf
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: output/stringtie/test.gene.abundance.txt
-      md5sum: 94b85145d60ab1b80a7f0f6cf08418b0
+      md5sum: f289f41b3ba1b9f0aa05d14408f1a5da
    - path: output/stringtie/test.transcripts.gtf
-      md5sum: 3196e3d50fd461aae6408e0a70acae68
+      md5sum: 9dcdc9577c0fdbb25089eda210267546
--- a/tests/modules/stringtie/stringtie/main.nf
+++ b/tests/modules/stringtie/stringtie/main.nf
@ -2,7 +2,7 @@

 nextflow.enable.dsl = 2

-include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
+include { STRINGTIE_STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
 //
 // Test with forward strandedness
 //
@ -13,7 +13,7 @@ workflow test_stringtie_forward {
    ]
    annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)

-    STRINGTIE ( input, annotation_gtf )
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
 }

 //
@ -26,5 +26,5 @@ workflow test_stringtie_reverse {
    ]
    annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)

-    STRINGTIE ( input, annotation_gtf )
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
 }
--- a/tests/modules/stringtie/stringtie/test.yml
+++ b/tests/modules/stringtie/stringtie/test.yml
@ -8,7 +8,6 @@
    - path: ./output/stringtie/test.gene.abundance.txt
      md5sum: 7d8bce7f2a922e367cedccae7267c22e
    - path: ./output/stringtie/test.coverage.gtf
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: ./output/stringtie/test.ballgown/e_data.ctab
      md5sum: 6b4cf69bc03f3f69890f972a0e8b7471
    - path: ./output/stringtie/test.ballgown/i_data.ctab
@ -30,7 +29,6 @@
    - path: ./output/stringtie/test.gene.abundance.txt
      md5sum: 7385b870b955dae2c2ab78a70cf05cce
    - path: ./output/stringtie/test.coverage.gtf
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: ./output/stringtie/test.ballgown/e_data.ctab
      md5sum: 879b6696029d19c4737b562e9d149218
    - path: ./output/stringtie/test.ballgown/i_data.ctab