Merge branch 'master' into vardict-java

modules/minimap2/align/main.nf

@@ -2,17 +2,21 @@ process MINIMAP2_ALIGN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
+    conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' :
-        'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' :
+        'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }"
 
     input:
     tuple val(meta), path(reads)
     path reference
+    val bam_format
+    val cigar_paf_format
+    val cigar_bam
 
     output:
-    tuple val(meta), path("*.paf"), emit: paf
+    tuple val(meta), path("*.paf"), optional: true, emit: paf
+    tuple val(meta), path("*.bam"), optional: true, emit: bam
     path "versions.yml"           , emit: versions
 
     when:
@@ -22,13 +26,19 @@ process MINIMAP2_ALIGN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
+    def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
+    def cigar_paf = cigar_paf_format && !sam_format ? "-c" : ''
+    def set_cigar_bam = cigar_bam && sam_format ? "-L" : ''
     """
     minimap2 \\
         $args \\
         -t $task.cpus \\
         $reference \\
         $input_reads \\
-        > ${prefix}.paf
+        $cigar_paf \\
+        $set_cigar_bam \\
+        $bam_output
+
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/minimap2/align/meta.yml

@@ -29,6 +29,17 @@ input:
       type: file
       description: |
         Reference database in FASTA format.
+  - bam_format:
+      type: boolean
+      description: Specify that output should be in BAM format
+  - cigar_paf_format:
+      type: boolean
+      description: Specify that output CIGAR should be in PAF format
+  - cigar_bam:
+      type: boolean
+      description: |
+        Write CIGAR with >65535 ops at the CG tag. This is recommended when
+        doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)
 output:
   - meta:
       type: map
@@ -39,9 +50,16 @@ output:
       type: file
       description: Alignment in PAF format
       pattern: "*.paf"
+  - bam:
+      type: file
+      description: Alignment in BAM format
+      pattern: "*.bam"
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
 authors:
   - "@heuermh"
+  - "@sofstam"
+  - "@sateeshperi"
+  - "@jfy133"

modules/trimgalore/main.nf

@@ -11,12 +11,13 @@ process TRIMGALORE {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("*.fq.gz")    , emit: reads
-    tuple val(meta), path("*report.txt"), emit: log
+    tuple val(meta), path("*{trimmed,val}*.fq.gz"), emit: reads
+    tuple val(meta), path("*report.txt")          , emit: log
     path "versions.yml"                           , emit: versions
 
-    tuple val(meta), path("*.html"), emit: html optional true
-    tuple val(meta), path("*.zip") , emit: zip optional true
+    tuple val(meta), path("*unpaired*.fq.gz")     , emit: unpaired, optional: true
+    tuple val(meta), path("*.html")               , emit: html    , optional: true
+    tuple val(meta), path("*.zip")                , emit: zip     , optional: true
 
     when:
     task.ext.when == null || task.ext.when
@@ -52,6 +53,7 @@ process TRIMGALORE {
             $c_r1 \\
             $tpc_r1 \\
             ${prefix}.fastq.gz
+
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
@@ -73,6 +75,7 @@ process TRIMGALORE {
             $tpc_r2 \\
             ${prefix}_1.fastq.gz \\
             ${prefix}_2.fastq.gz
+
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')

modules/trimgalore/meta.yml

@@ -37,6 +37,11 @@ output:
         List of input adapter trimmed FastQ files of size 1 and 2 for
         single-end and paired-end data, respectively.
       pattern: "*.{fq.gz}"
+  - unpaired:
+      type: file
+      description: |
+        FastQ files containing unpaired reads from read 1 or read 2
+      pattern: "*unpaired*.fq.gz"
   - html:
       type: file
       description: FastQC report (optional)

tests/modules/minimap2/align/main.nf

@@ -9,8 +9,11 @@ workflow test_minimap2_align_single_end {
               [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    bam_format = true
+    cigar_paf_format = false
+    cigar_bam = false
 
-    MINIMAP2_ALIGN ( input, fasta )
+    MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam)
 }
 
 workflow test_minimap2_align_paired_end {
@@ -19,6 +22,9 @@ workflow test_minimap2_align_paired_end {
                 file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    bam_format  = true
+    cigar_paf_format = false
+    cigar_bam = false
 
-    MINIMAP2_ALIGN ( input, fasta )
+    MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam )
 }

tests/modules/minimap2/align/test.yml

@@ -1,17 +1,17 @@
-- name: minimap2 align single-end
-  command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/minimap2/align/nextflow.config
+- name: minimap2 align test_minimap2_align_single_end
+  command: nextflow run tests/modules/minimap2/align -entry test_minimap2_align_single_end -c tests/config/nextflow.config
   tags:
     - minimap2
     - minimap2/align
   files:
-    - path: ./output/minimap2/test.paf
-      md5sum: 70e8cf299ee3ecd33e629d10c1f588ce
+    - path: output/minimap2/test.bam
+    - path: output/minimap2/versions.yml
 
-- name: minimap2 align paired-end
-  command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/minimap2/align/nextflow.config
+- name: minimap2 align test_minimap2_align_paired_end
+  command: nextflow run tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c tests/config/nextflow.config
   tags:
     - minimap2
     - minimap2/align
   files:
-    - path: ./output/minimap2/test.paf
-      md5sum: 5e7b55a26bf0ea3a2843423d3e0b9a28
+    - path: output/minimap2/test.bam
+    - path: output/minimap2/versions.yml