fix: CI is working

software/bwamem2/index/main.nf

@@ -28,8 +28,8 @@ process BWAMEM2_INDEX {
     script:
     def software = getSoftwareName(task.process)
     """
-    mkdir bwa
-    bwa-mem2 index $ioptions.args $fasta -p bwamem2/${fasta.baseName}
+    mkdir bwamem2
+    bwa-mem2 index $options.args $fasta -p bwamem2/${fasta}
     echo \$(bwa-mem2 version 2>&1) > ${software}.version.txt
     """
 }

software/bwamem2/mem/main.nf

@@ -21,6 +21,7 @@ process BWAMEM2_MEM {
     input:
     tuple val(meta), path(reads)
     path  index
+    path  fasta
 
     output:
     tuple val(meta), path("*.bam"), emit: bam

tests/data/index/E_coli/bwamem2/NC_010473.fa.amb

@@ -0,0 +1,3 @@
+4686137 1 2
+20895 1 Y
+142347 1 R

tests/data/index/E_coli/bwamem2/NC_010473.fa.ann

@@ -0,0 +1,3 @@
+4686137 1 11
+0 gi|170079663|ref|NC_010473.1| Escherichia coli str. K-12 substr. DH10B, complete genome
+0 4686137 2

tests/software/bwamem2/index/main.nf

@@ -0,0 +1,9 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWAMEM2_INDEX } from '../../../../software/bwamem2/index/main.nf' addParams( options: [:] )
+
+workflow test_bwamem2_index {
+    BWAMEM2_INDEX ( file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) )
+}

tests/software/bwamem2/index/test.yml

@@ -0,0 +1,16 @@
+- name: bwamem2 index
+  command: nextflow run ./tests/software/bwamem2/index -entry test_bwamem2_index -c tests/config/nextflow.config
+  tags:
+    - bwamem2
+    - bwamem2_index
+  files:
+    - path: output/bwamem2/bwamem2/NC_010473.fa.0123
+      md5sum: e112e4d2fd893fb939d306b27ece9de5
+    - path: output/bwamem2/bwamem2/NC_010473.fa.amb
+      md5sum: 942a990ae872f1c0b8d72dda2db405d5
+    - path: output/bwamem2/bwamem2/NC_010473.fa.ann
+      md5sum: ebf1a0279cf5b8d7f1a8cb855a3a3705
+    - path: output/bwamem2/bwamem2/NC_010473.fa.bwt.2bit.64
+      md5sum: f0154573be12440aee294b726cd88c86
+    - path: output/bwamem2/bwamem2/NC_010473.fa.pac
+      md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad

tests/software/bwamem2/mem/main.nf

@@ -0,0 +1,38 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWAMEM2_MEM } from '../../../../software/bwamem2/mem/main.nf' addParams( options: [:] )
+
+/*
+ * Test with single-end data
+ */
+workflow test_bwamem2_mem_single_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
+
+    BWAMEM2_MEM (
+        input,
+        file("${launchDir}/tests/data/index/E_coli/bwamem2/", checkIfExists: true),
+        file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    )
+}
+
+/*
+ * Test with paired-end data
+ */
+workflow test_bwamem2_mem_paired_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
+
+    BWAMEM2_MEM (
+        input,
+        file("${launchDir}/tests/data/index/E_coli/bwamem2/", checkIfExists: true),
+        file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    )
+}

tests/software/bwamem2/mem/test.yml

@@ -0,0 +1,19 @@
+- name: bwamem2 mem single-end
+  command: nextflow run ./tests/software/bwamem2/mem -entry test_bwamem2_mem_single_end -c tests/config/nextflow.config
+  tags:
+    - bwamem2
+    - bwamem2_mem
+    - bwamem2_mem_single_end
+  files:
+    - path: output/bwamem2/test.bam
+      md5sum: 354acd3b7033a2d4ee69452df18c0a4d
+
+- name: bwamem2 mem paired-end
+  command: nextflow run ./tests/software/bwamem2/mem -entry test_bwamem2_mem_paired_end -c tests/config/nextflow.config
+  tags:
+    - bwamem2
+    - bwamem2_mem
+    - bwamem2_mem_paired_end
+  files:
+    - path: output/bwamem2/test.bam
+      md5sum: 26187528a7bde13a2a9e9dd549b9bcd0