takes gunzip out of fargene main.nf (#1090)

* takes gunzip out of fargene main.nf

* update definition of input

* options.args -> args

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

modules/fargene/main.nf

@@ -35,15 +35,12 @@ process FARGENE {
     def args = task.ext.args ?: ''
     prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
-    gzip \\
+    fargene \\
-        -cdf $input \\
+        $args \\
-        > unziped.fa |
+        -p $task.cpus \\
-        fargene \\
+        -i $input \\
-            $args \\
+        --hmm-model $hmm_model \\
-            -p $task.cpus \\
+        -o $prefix
-            -i unziped.fa \\
-            --hmm-model $hmm_model \\
-            -o $prefix
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/fargene/meta.yml

@@ -23,7 +23,7 @@ input:
         e.g. [ id:'test', single_end:false ]
   - input:
       type: file
-      description: fasta or paired-end fastq file containing either genomes or longer contigs as nucleotide or protein sequences (fasta) or fragmented metagenomic reads (fastq)
+      description: uncompressed fasta file or paired-end fastq files containing either genomes or longer contigs as nucleotide or protein sequences (fasta) or fragmented metagenomic reads (fastq)
       pattern: "*.{fasta}"
   - hmm_model:
       type: string

tests/modules/fargene/main.nf

@@ -2,6 +2,7 @@
 
 nextflow.enable.dsl = 2
 
+include { GUNZIP } from '../../../modules/gunzip/main.nf'
 include { FARGENE } from '../../../modules/fargene/main.nf'
 
 workflow test_fargene {
@@ -10,5 +11,6 @@ workflow test_fargene {
               file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true) ]
     hmm_model = 'class_a'
 
-    FARGENE ( input, hmm_model )
+    GUNZIP ( input )
+    FARGENE ( GUNZIP.out.gunzip, hmm_model )
 }

tests/modules/fargene/test.yml

@@ -4,9 +4,11 @@
     - fargene
   files:
     - path: output/fargene/fargene_analysis.log
-    - path: output/fargene/test/hmmsearchresults/unziped-class_A-hmmsearched.out
+    - path: output/fargene/test/hmmsearchresults/test1.contigs-class_A-hmmsearched.out
     - path: output/fargene/test/results_summary.txt
       md5sum: 690d351cfc52577263ef4cfab1c81f50
-    - path: output/fargene/test/tmpdir/tmp.out
+    - path: output/fargene/test/tmpdir/test1.contigs-positives.out
-    - path: output/fargene/test/tmpdir/unziped-positives.out
       md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/fargene/test/tmpdir/tmp.out
+    - path: output/gunzip/test1.contigs.fa
+      md5sum: 80c4d78f2810f6d9e90fa6da9bb9c4f9