Patch fix artic/minion and ivar/variants modules (#1326)

modules/artic/minion/main.nf

@@ -13,7 +13,8 @@ process ARTIC_MINION {
     path  sequencing_summary
     path  ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.reference.fasta")
     path  ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.scheme.bed")
-    path  medaka_model
+    path  medaka_model_file
+    val   medaka_model_string
     val   scheme
     val   scheme_version
 
@@ -44,7 +45,7 @@ process ARTIC_MINION {
     if (args.tokenize().contains('--medaka')) {
         fast5   = ""
         summary = ""
-        model = file(medaka_model).exists() ? "--medaka-model ./$medaka_model" : "--medaka-model $medaka_model"
+        model   = medaka_model_file ? "--medaka-model ./$medaka_model_file" : "--medaka-model $medaka_model_string"
     }
     def hd5_plugin_path = task.ext.hd5_plugin_path ? "export HDF5_PLUGIN_PATH=" + task.ext.hd5_plugin_path : "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin"
     """

modules/artic/minion/meta.yml

@@ -42,11 +42,16 @@ input:
         bed files containing coordinates of each primer in the scheme,
         relative to the reference genome
       pattern: "*.{scheme.bed}"
-  - medaka_model:
+  - medaka_model_file:
       type: file
       description: |
-        Medaka model to use (if option --medaka is set)
-      pattern: "*.*"
+        Medaka model file to use (if option --medaka is set)
+      pattern: "*.hdf5"
+  - medaka_model_string:
+      type: value
+      description: |
+        Medaka model string to use (if option --medaka is set)
+      pattern: "*"
   - scheme:
       type: value
       description: Name of the primer scheme

modules/ivar/variants/main.nf

@@ -10,6 +10,7 @@ process IVAR_VARIANTS {
     input:
     tuple val(meta), path(bam)
     path  fasta
+    path  fai
     path  gff
     val   save_mpileup
 

modules/ivar/variants/meta.yml

@@ -25,6 +25,10 @@ input:
       type: file
       description: The reference sequence used for mapping and generating the BAM file
       pattern: "*.fa"
+  - fai:
+      type: file
+      description: The index for the reference sequence used for mapping and generating the BAM file
+      pattern: "*.fai"
   - gff:
       type: file
       description: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.

tests/modules/artic/minion/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { UNTAR } from '../../../../modules/untar/main.nf'
+include { UNTAR        } from '../../../../modules/untar/main.nf'
 include { ARTIC_MINION } from '../../../../modules/artic/minion/main.nf'
 
 workflow test_artic_minion {
@@ -15,9 +15,8 @@ workflow test_artic_minion {
     sequencing_summary = file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true)
     fasta              = file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta', checkIfExists: true)
     bed                = file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed', checkIfExists: true)
-    dummy_file         = []
 
     fast5_dir = UNTAR ( fast5_tar ).untar
 
-    ARTIC_MINION ( input, fast5_dir, sequencing_summary, fasta, bed, dummy_file, 'nCoV-2019', '3')
+    ARTIC_MINION ( input, fast5_dir, sequencing_summary, fasta, bed, [], '', 'nCoV-2019', '3')
 }

tests/modules/ivar/variants/main.nf

@@ -11,10 +11,11 @@ workflow test_ivar_variants_no_gff_no_mpileup {
         file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
     ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    gff = []
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    gff   = []
     save_mpileup = false
 
-    IVAR_VARIANTS ( input, fasta, gff, save_mpileup )
+    IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup )
 }
 
 workflow test_ivar_variants_no_gff_with_mpileup {
@@ -24,10 +25,11 @@ workflow test_ivar_variants_no_gff_with_mpileup {
         file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
     ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    gff = []
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    gff   = []
     save_mpileup = true
 
-    IVAR_VARIANTS ( input, fasta, gff, save_mpileup )
+    IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup )
 }
 
 workflow test_ivar_variants_with_gff_with_mpileup {
@@ -37,8 +39,9 @@ workflow test_ivar_variants_with_gff_with_mpileup {
         file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
     ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    gff   = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
     save_mpileup = true
 
-    IVAR_VARIANTS ( input, fasta, gff, save_mpileup )
+    IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup )
 }