Merge branch 'master' into update/mosdepth

modules/gamma/gamma/main.nf

@@ -1,6 +1,6 @@
 def VERSION = '2.1' // Version information not provided by tool on CLI
 
-process GAMMA {
+process GAMMA_GAMMA {
     tag "$meta.id"
     label 'process_low'
 
@@ -26,13 +26,24 @@ process GAMMA {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+
     """
-    GAMMA.py \\
+    if [[ ${fasta} == *.gz ]]
+    then
+        FNAME=\$(basename ${fasta} .gz)
+        gunzip -f ${fasta}
+        GAMMA.py \\
+        $args \\
+        "\${FNAME}" \\
+        $db \\
+        $prefix
+    else
+        GAMMA.py \\
         $args \\
         $fasta \\
         $db \\
         $prefix
-
+    fi
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         gamma: $VERSION

modules/gamma/gamma/meta.yml

@@ -1,4 +1,4 @@
-name: "gamma"
+name: "gamma_gamma"
 description: Gene Allele Mutation Microbial Assessment
 keywords:
   - gamma
@@ -61,3 +61,4 @@ output:
 authors:
   - "@sateeshperi"
   - "@rastanton"
+  - "@jvhagey"

modules/mash/screen/main.nf

@@ -8,8 +8,8 @@ process MASH_SCREEN {
         'quay.io/biocontainers/mash:2.3--he348c14_1' }"
 
     input:
-    tuple val(meta), path(query_sketch)
-    path fastx_db
+    tuple val(meta), path(query)
+    path sequences_sketch
 
     output:
     tuple val(meta), path("*.screen"), emit: screen
@@ -26,8 +26,8 @@ process MASH_SCREEN {
         screen \\
         $args \\
         -p $task.cpus \\
-        $query_sketch \\
-        $fastx_db \\
+        $sequences_sketch \\
+        $query \\
         > ${prefix}.screen
 
     cat <<-END_VERSIONS > versions.yml

modules/mash/screen/meta.yml

@@ -20,13 +20,14 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - query_sketch:
+  - query:
       type: file
-      description: MinHash sketch of query sequences
-      pattern: "*.msh"
-  - fastx_db:
+      description: Query sequences
+      pattern: "*.fastq.gz"
+  - sequence_sketch:
       type: file
       description: Sequence files to match against
+      pattern: "*.msh"
 
 output:
   - meta:

tests/config/pytest_modules.yml

@@ -711,9 +711,9 @@ freebayes:
   - modules/freebayes/**
   - tests/modules/freebayes/**
 
-gamma:
-  - modules/gamma/**
-  - tests/modules/gamma/**
+gamma/gamma:
+  - modules/gamma/gamma/**
+  - tests/modules/gamma/gamma/**
 
 gatk4/applybqsr:
   - modules/gatk4/applybqsr/**

tests/modules/gamma/gamma/main.nf

@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GAMMA_GAMMA } from '../../../../modules/gamma/gamma/main.nf'
+
+workflow test_unzip {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true),
+    ]
+
+    db = [ file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/ResGANNCBI_20210507_srst2.fasta", checkIfExists: true), ]
+
+    GAMMA_GAMMA ( input, db )
+}
+
+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_GAMMA ( input, db )
+}

tests/modules/gamma/gamma/test.yml

@@ -0,0 +1,29 @@
+- name: gamma gamma test_unzip
+  command: nextflow run tests/modules/gamma/gamma -entry test_unzip -c tests/config/nextflow.config
+  tags:
+    - gamma/gamma
+    - gamma
+  files:
+    - path: output/gamma/test.fasta
+      md5sum: 5b3b831d863fffaa3410a9ee7bfa12ce
+    - path: output/gamma/test.gamma
+      md5sum: 46165a89e10b7315d3a9b0aa6c561626
+    - path: output/gamma/test.psl
+      md5sum: f489ce4602ddbcb692d5781ee3fbf449
+    - path: output/gamma/versions.yml
+      md5sum: 8baafec7b3b87f788f69e30d317c9722
+
+- name: gamma gamma test_gamma
+  command: nextflow run tests/modules/gamma/gamma -entry test_gamma -c tests/config/nextflow.config
+  tags:
+    - gamma/gamma
+    - 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: b75c2871d8cac2f8ac67c0fbd22babd6

tests/modules/gamma/main.nf

@@ -1,17 +0,0 @@
-#!/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 )
-}

tests/modules/gamma/test.yml

@@ -1,13 +0,0 @@
-- 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

tests/modules/mash/screen/main.nf

@@ -14,8 +14,11 @@ workflow test_mash_screen {
             file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
         ]
     ]
-    fastx_db = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    sars_db = [
+        [ id: 'sars_db' ],
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
 
-    MASH_SKETCH ( input )
-    MASH_SCREEN ( MASH_SKETCH.out.mash, fastx_db )
+    MASH_SKETCH ( sars_db )
+    MASH_SCREEN ( input, MASH_SKETCH.out.mash.map { meta, sketch -> sketch } )
 }

tests/modules/mash/screen/test.yml

@@ -4,9 +4,9 @@
     - mash
     - mash/screen
   files:
-    - path: output/mash/test.mash_stats
-      md5sum: 2a6f297d8e69a5e4160243bc6c89129c
-    - path: output/mash/test.msh
-      md5sum: d747145a43dad5f82342036f8f5d9133
+    - path: output/mash/sars_db.mash_stats
+      md5sum: 1dafbd23e36e18bf4c87a007d0fc98f7
+    - path: output/mash/sars_db.msh
+      md5sum: 24289e4a13526e88eeb2abfca4a0f0a8
     - path: output/mash/test.screen
-      md5sum: d3c871dccd5cd57ab54781fa5c5d7278
+      md5sum: ac8701e1aab651b2f36c6380b1351b11