Merge branch 'master' into new-module-hap.py

modules/bowtie2/align/main.nf

@@ -29,6 +29,8 @@ process BOWTIE2_ALIGN {
         def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
         """
         INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
+        [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`
+        [ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
         bowtie2 \\
             -x \$INDEX \\
             -U $reads \\
@@ -49,6 +51,8 @@ process BOWTIE2_ALIGN {
         def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
         """
         INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
+        [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`
+        [ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
         bowtie2 \\
             -x \$INDEX \\
             -1 ${reads[0]} \\

modules/vardictjava/main.nf

@@ -10,8 +10,7 @@ process VARDICTJAVA {
         'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(bam), path(bai)
-    path(bed)
+    tuple val(meta), path(bam), path(bai), path(bed)
     tuple path(fasta), path(fasta_fai)
 
     output:

tests/modules/bowtie2/align/main.nf

@@ -32,4 +32,4 @@ workflow test_bowtie2_align_paired_end {
 
     BOWTIE2_BUILD ( fasta )
     BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
-}
+}

tests/modules/bowtie2/align/nextflow.config

@@ -1,5 +1,16 @@
+params {
+    force_large_index = false
+}
+
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
+}
+
+if (params.force_large_index) {
+    process {
+        withName: BOWTIE2_BUILD {
+            ext.args = '--large-index'
+        }
+    }
 }

tests/modules/bowtie2/align/test.yml

@@ -39,3 +39,45 @@
       md5sum: 52be6950579598a990570fbcf5372184
     - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
       md5sum: e3b4ef343dea4dd571642010a7d09597
+
+- name: bowtie2 align single-end large-index
+  command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config --force_large_index
+  tags:
+    - bowtie2
+    - bowtie2/align
+  files:
+    - path: ./output/bowtie2/test.bam
+    - path: ./output/bowtie2/test.bowtie2.log
+    - path: ./output/bowtie2/bowtie2/genome.3.bt2l
+      md5sum: 8952b3e0b1ce9a7a5916f2e147180853
+    - path: ./output/bowtie2/bowtie2/genome.2.bt2l
+      md5sum: 22c284084784a0720989595e0c9461fd
+    - path: ./output/bowtie2/bowtie2/genome.1.bt2l
+      md5sum: 07d811cd4e350d56267183d2ac7023a5
+    - path: ./output/bowtie2/bowtie2/genome.4.bt2l
+      md5sum: c25be5f8b0378abf7a58c8a880b87626
+    - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2l
+      md5sum: fda48e35925fb24d1c0785f021981e25
+    - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2l
+      md5sum: 802c26d32b970e1b105032b7ce7348b4
+
+- name: bowtie2 align paired-end large-index
+  command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config --force_large_index
+  tags:
+    - bowtie2
+    - bowtie2/align
+  files:
+    - path: ./output/bowtie2/test.bam
+    - path: ./output/bowtie2/test.bowtie2.log
+    - path: ./output/bowtie2/bowtie2/genome.3.bt2l
+      md5sum: 8952b3e0b1ce9a7a5916f2e147180853
+    - path: ./output/bowtie2/bowtie2/genome.2.bt2l
+      md5sum: 22c284084784a0720989595e0c9461fd
+    - path: ./output/bowtie2/bowtie2/genome.1.bt2l
+      md5sum: 07d811cd4e350d56267183d2ac7023a5
+    - path: ./output/bowtie2/bowtie2/genome.4.bt2l
+      md5sum: c25be5f8b0378abf7a58c8a880b87626
+    - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2l
+      md5sum: fda48e35925fb24d1c0785f021981e25
+    - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2l
+      md5sum: 802c26d32b970e1b105032b7ce7348b4

tests/modules/vardictjava/main.nf

@@ -9,15 +9,14 @@ workflow test_vardictjava {
     bam_input_ch = Channel.value([
         [ id:'test' ], // meta map
         file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
     ])
 
-    bed = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true))
-
     reference = Channel.value([
         file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
         file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     ])
 
-    VARDICTJAVA ( bam_input_ch, bed, reference )
+    VARDICTJAVA ( bam_input_ch, reference )
 }