Merge pull request #246 from drpatelh/master

Update iVar modules

software/ivar/consensus/main.nf

@@ -34,7 +34,7 @@ process IVAR_CONSENSUS {
     def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
     """
     samtools mpileup \\
-        --fasta-ref $fasta \\
+        --reference $fasta \\
         $options.args2 \\
         $bam | \\
         $save_mpileup \\

software/ivar/trim/main.nf

@@ -19,11 +19,12 @@ process IVAR_TRIM {
     }
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam), path(bai)
     path bed
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path('*.log'), emit: log
     path "*.version.txt"          , emit: version
 
     script:
@@ -34,7 +35,8 @@ process IVAR_TRIM {
         $options.args \\
         -i $bam \\
         -b $bed \\
-        -p $prefix
+        -p $prefix \\
+        > ${prefix}.ivar.log
 
     ivar version | head -n1 2>&1 | sed 's/^.*iVar version //g' > ${software}.version.txt
     """

software/ivar/trim/meta.yml

@@ -39,8 +39,12 @@ input:
             e.g. [ id:'test', single_end:false ]
     - bam:
         type: file
-        description: A sorted (with samtools sort) bam file
+        description: Co-ordinate sorted BAM file
         pattern: "*.bam"
+    - bai:
+        type: file
+        description: Index file for co-ordinate sorted BAM file
+        pattern: "*.bai"
     - bed:
         type: file
         description: BED file with primer labels and positions
@@ -55,6 +59,10 @@ output:
         type: file
         description: iVar generated trimmed bam file (unsorted)
         pattern: "*.bam"
+    - log:
+        type: file
+        description: Log file generated by iVar for use with MultiQC
+        pattern: "*.log"
     - version:
         type: file
         description: File containing software version

tests/software/ivar/trim/main.nf

@@ -5,11 +5,12 @@ nextflow.enable.dsl = 2
 include { IVAR_TRIM } from '../../../../software/ivar/trim/main.nf' addParams([:])
 
 workflow test_ivar_trim {
-    bed_file = file("${launchDir}/tests/data/bed/test-sc2-artic-v3.bed", checkIfExists: true)
+    def bed = file("${launchDir}/tests/data/bed/test-sc2-artic-v3.bed", checkIfExists: true)
 
     def input = []
-    input = [ [ id:'test'], 
+    input = [ [ id:'test'],
-                file("${launchDir}/tests/data/bam/test-sc2-artic-v3.bam", checkIfExists: true) ]
+                file("${launchDir}/tests/data/bam/test-sc2-artic-v3.bam", checkIfExists: true),
+                file("${launchDir}/tests/data/bam/test-sc2-artic-v3.bam.bai", checkIfExists: true) ]
 
-    IVAR_TRIM ( input, bed_file )
+    IVAR_TRIM ( input, bed )
 }