Add fasta/gff input option

modules/antismash/antismashlite/main.nf

@@ -1,3 +1,76 @@
+// process ANTISMASH_ANTISMASHLITE {
+//     tag "$meta.id"
+//     label 'process_medium'
+
+//     conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null)
+//     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+//         'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' :
+//         'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
+
+//     containerOptions {
+//         workflow.containerEngine == 'singularity' ?
+//         "-B $antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" :
+//         workflow.containerEngine == 'docker' ?
+//         "-v \$PWD/$antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" :
+//         ''
+//         }
+
+//     input:
+//     tuple val(meta), path(sequence_input)
+//     path(databases)
+//     path(antismash_dir) // Optional input: AntiSMASH installation folder. It is not needed for using this module with conda, but required for docker/singularity (see meta.yml).
+
+//     output:
+//     tuple val(meta), path("${prefix}/clusterblast/*_c*.txt")                 , optional: true, emit: clusterblast_file
+//     tuple val(meta), path("${prefix}/css/*.css")                             , emit: css_file
+//     tuple val(meta), path("${prefix}/images")                                , emit: image_directory
+//     tuple val(meta), path("${prefix}/js/*.js")                               , emit: javascript
+//     tuple val(meta), path("${prefix}/knownclusterblast/region*/ctg*.html")   , optional: true, emit: knownclusterblast_html
+//     tuple val(meta), path("${prefix}/knownclusterblast/*_c*.txt")            , optional: true, emit: knownclusterblast_txt
+//     tuple val(meta), path("${prefix}/svg/clusterblast*.svg")                 , optional: true, emit: svg_files_clusterblast
+//     tuple val(meta), path("${prefix}/svg/knownclusterblast*.svg")            , optional: true, emit: svg_files_knownclusterblast
+//     tuple val(meta), path("${prefix}/*.gbk")                                 , emit: gbk_input
+//     tuple val(meta), path("${prefix}/*.json")                                , emit: json_results
+//     tuple val(meta), path("${prefix}/*.log")                                 , emit: log
+//     tuple val(meta), path("${prefix}/*.zip")                                 , emit: zip
+//     tuple val(meta), path("${prefix}/*region*.gbk")                          , emit: gbk_results
+//     tuple val(meta), path("${prefix}/clusterblastoutput.txt")                , optional: true, emit: clusterblastoutput
+//     tuple val(meta), path("${prefix}/index.html")                            , emit: html
+//     tuple val(meta), path("${prefix}/knownclusterblastoutput.txt")           , optional: true, emit: knownclusterblastoutput
+//     tuple val(meta), path("${prefix}/regions.js")                            , emit: json_sideloading
+//     path "versions.yml"                                                      , emit: versions
+
+//     when:
+//     task.ext.when == null || task.ext.when
+
+//     script:
+//     def args = task.ext.args ?: ''
+//     prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+//     // if ( sequence_input.getExtension != 'fasta' && sequence_input.getExtension != 'fna' && gff )
+//     //     log.warn "GFF input to antiSMASH can only be used if FASTA sequence input is supplied. GFF will be ignored for sample ${meta.id}"
+//     // if ( (sequence_input.getExtension == 'fasta' || sequence_input.getExtension == 'fna') && gff )
+//     //     gff_flag = "--genefinding-gff3 ${gff}"
+//     // else
+//     //     gff_flag = ""
+
+//     """
+//     ## We specifically do not include annotations (--genefinding-tool none) as
+//     ## this should be run as a separate module for versioning purposes
+//     antismash \\
+//         $args \\
+//         -c $task.cpus \\
+//         --output-dir $prefix \\
+//         --genefinding-tool none \\
+//         --logfile $prefix/${prefix}.log \\
+//         --databases $databases \\
+//         $sequence_input
+
+//     cat <<-END_VERSIONS > versions.yml
+//     "${task.process}":
+//         antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
+//     END_VERSIONS
+//     """
+// }
 process ANTISMASH_ANTISMASHLITE {
     tag "$meta.id"
     label 'process_medium'
@@ -17,9 +90,9 @@ process ANTISMASH_ANTISMASHLITE {
 
     input:
     tuple val(meta), path(sequence_input)
-    path(gff)
     path(databases)
     path(antismash_dir) // Optional input: AntiSMASH installation folder. It is not needed for using this module with conda, but required for docker/singularity (see meta.yml).
+    path(gff)
 
     output:
     tuple val(meta), path("${prefix}/clusterblast/*_c*.txt")                 , optional: true, emit: clusterblast_file
@@ -47,24 +120,19 @@ process ANTISMASH_ANTISMASHLITE {
     script:
     def args = task.ext.args ?: ''
     prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
-    if ( sequence_input.getExtension != 'fasta' && sequence_input.getExtension != 'fna' && gff )
-        log.warn "GFF input to antiSMASH can only be used if FASTA sequence input is supplied. GFF will be ignored for sample ${meta.id}"
-    if ( (sequence_input.getExtension == 'fasta' || sequence_input.getExtension == 'fna') && gff )
     gff_flag = "--genefinding-gff3 ${gff}"
-    else
-        gff_flag = ""
 
     """
     ## We specifically do not include annotations (--genefinding-tool none) as
     ## this should be run as a separate module for versioning purposes
     antismash \\
         $args \\
+        $gff_flag \\
         -c $task.cpus \\
         --output-dir $prefix \\
         --genefinding-tool none \\
         --logfile $prefix/${prefix}.log \\
         --databases $databases \\
-        $gff_flag \\
         $sequence_input
 
     cat <<-END_VERSIONS > versions.yml

modules/antismash/antismashlite/meta.yml

@@ -35,10 +35,6 @@ input:
       type: file
       description: nucleotide sequence file (annotated)
       pattern: "*.{gbk, gb, gbff, genbank, embl, fasta, fna}"
-  - gff:
-      type: file
-      description: GFF3 file to extract annotated features from (only needed if sequence_input is in FASTA format)
-      pattern: "*.{gff, GFF}"
   - databases:
       type: directory
       description: downloaded AntiSMASH databases e.g. data/databases
@@ -53,6 +49,9 @@ input:
         directory needs to be mounted (including all modified files from the downloading step)
         to the container as a workaround.
       pattern: "*"
+  - gff:
+    type: file
+    pattern: "*.gff"
 
 output:
   - meta:

tests/modules/antismash/antismashlite/main.nf

@@ -2,35 +2,106 @@
 
 nextflow.enable.dsl = 2
 
+include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/antismash/antismashlite/main.nf'
+include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/antismash/antismashlitedownloaddatabases/main.nf'
+include { GUNZIP as GUNZIP1 } from '../../../../modules/gunzip/main.nf'
+include { GUNZIP as GUNZIP2 } from '../../../../modules/gunzip/main.nf'
 include { UNTAR as UNTAR1 } from '../../../../modules/untar/main.nf'
 include { UNTAR as UNTAR2 } from '../../../../modules/untar/main.nf'
 include { UNTAR as UNTAR3 } from '../../../../modules/untar/main.nf'
-include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/antismash/antismashlitedownloaddatabases/main.nf'
-include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/antismash/antismashlite/main.nf'
 
 workflow test_antismashlite {
-    input_genome = [
+    genome_fna = [
-        [ id:'test' ], // meta map
+        [ id:'test' ],
-        file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true) ]
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+    ]
 
-    input_antismash_db1 = [
+    genome_gff = [
+        [],
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_gff_gz'], checkIfExists: true)
+    ]
+
+    antismash_db1 = [
         [],
         file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
     ]
 
-    input_antismash_db2 = [
+    antismash_db2 = [
         [],
         file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
     ]
 
-    input_antismash_db3 = [
+    antismash_db3 = [
         [],
         file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
     ]
 
-    UNTAR1 ( input_antismash_db1 )
+    // input_db = [
-    UNTAR2 ( input_antismash_db2 )
+    //     file('/home/jasmin/antismash_db/', checkIfExists: true)
-    UNTAR3 ( input_antismash_db3 )
+    // ]
+
+    // input_dir = [
+    //     file('/home/jasmin/antismash_dir/', checkIfExists: true)
+    // ]
+
+    GUNZIP1 ( genome_fna )
+    GUNZIP2 ( genome_gff )
+    UNTAR1 ( antismash_db1 )
+    UNTAR2 ( antismash_db2 )
+    UNTAR3 ( antismash_db3 )
     ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] },  UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
-    ANTISMASH_ANTISMASHLITE ( input_genome, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir, [] )
+    ANTISMASH_ANTISMASHLITE ( GUNZIP1.out.gunzip, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir, GUNZIP2.out.gunzip.map{ it[1] } )
+    // ANTISMASH_ANTISMASHLITE ( GUNZIP1.out.gunzip, input_db, input_dir, GUNZIP2.out.gunzip.map{ it[1] } )
+
 }
+// #!/usr/bin/env nextflow
+
+// nextflow.enable.dsl = 2
+
+// // include { UNTAR as UNTAR1 } from '../../../../modules/untar/main.nf'
+// // include { UNTAR as UNTAR2 } from '../../../../modules/untar/main.nf'
+// // include { UNTAR as UNTAR3 } from '../../../../modules/untar/main.nf'
+// // // include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/antismash/antismashlitedownloaddatabases/main.nf'
+// include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/antismash/antismashlite/main.nf'
+
+// workflow test_antismashlite {
+//     input_genome = [
+//         [ id:'test' ], // meta map
+//         file('/home/jasmin/Downloads/BAN001-megahit.gbk', checkIfExists: true) ]
+
+//     // input_antismash_db1 = [
+//     //     [],
+//     //     file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
+//     // ]
+
+//     // input_antismash_db2 = [
+//     //     [],
+//     //     file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
+//     // ]
+
+//     // input_antismash_db3 = [
+//     //     [],
+//     //     file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
+//     // ]
+
+//     input_db = [
+//         [],
+//         file('/home/jasmin/antismash_db/', checkIfExists: true)
+//     ]
+
+//     input_dir = [
+//         [],
+//         file('/home/jasmin/antismash_dir', checkIfExists: true)
+//     ]
+
+//     // input_gff = [
+//     //     [],
+//     //     file('/home/jasmin/Downloads/BAN001.gff', checkIfExists: true)
+//     // ]
+
+//     // UNTAR1 ( input_antismash_db1 )
+//     // UNTAR2 ( input_antismash_db2 )
+//     // UNTAR3 ( input_antismash_db3 )
+//     // ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] },  UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
+//     ANTISMASH_ANTISMASHLITE ( input_genome, input_db, input_dir )
+// }

tests/modules/antismash/antismashlite/test.yml

@@ -13,11 +13,10 @@
     - path: output/antismash/test/genome.gbk
       contains: ['/tool="antismash"']
     - path: output/antismash/test/genome.json
-      contains:
+      contains: ['{"version": "6.0.1", "input_file": "genome.fna.gz", "records": [{"id": "NZ_CP069563.1", "seq": {"data":']
-        ['{"version": "6.0.1", "input_file": "genome.gbff.gz", "records": [{"id": "NZ_CP069563.1", "seq": {"data":']
     - path: output/antismash/test/genome.zip
     - path: output/antismash/test/index.html
-      md5sum: 32aaf51315258af3b300d9a5bafd7bdc
+      md5sum: de787e865c3a1eec143a19d2facb4de4
     - path: output/antismash/test/js/antismash.js
       md5sum: 58e90c3d783ae014cc3d51849bcb50a2
     - path: output/antismash/test/js/jquery.js
@@ -30,3 +29,17 @@
       contains: ["antiSMASH version: 6.0.1"]
     - path: output/antismash/versions.yml
       md5sum: 759431a43da33e2ef8e2d0ebd79a439b
+    - path: output/gunzip1/genome.fna
+      md5sum: dafd38f5454b54fbea38245d773062a5
+    - path: output/gunzip1/versions.yml
+      md5sum: 854e3d45d43d2bc3bedf4bd6586e3e1f
+    - path: output/gunzip2/genome.gff
+      md5sum: 9b9c848b1946d43fa68128f4d6316052
+    - path: output/gunzip2/versions.yml
+      md5sum: 67bdab99aaaf1edfc0869bd2e6808036
+    - path: output/untar1/versions.yml
+      md5sum: 1e4721017721c45370996318e6b807e5
+    - path: output/untar2/versions.yml
+      md5sum: a6ae4977a432f3c5ef26687cec8622de
+    - path: output/untar3/versions.yml
+      md5sum: a5ee00c1c426ed601ff654891ba0f645