add qualimap with cram files + remove val from qualimap/bam, instead use empty list as everywhere else (#1320)

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>

modules/qualimap/bamqc/main.nf

@@ -10,7 +10,6 @@ process QUALIMAP_BAMQC {
     input:
     tuple val(meta), path(bam)
     path gff
-    val use_gff
 
     output:
     tuple val(meta), path("${prefix}"), emit: results
@@ -25,7 +24,7 @@ process QUALIMAP_BAMQC {
 
     def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs'
     def memory     = task.memory.toGiga() + "G"
-    def regions = use_gff ? "--gff $gff" : ''
+    def regions = gff ? "--gff $gff" : ''
 
     def strandedness = 'non-strand-specific'
     if (meta.strandedness == 'forward') {

modules/qualimap/bamqc/meta.yml

@@ -29,9 +29,6 @@ input:
       type: file
       description: Feature file with regions of interest
       pattern: "*.{gff,gtf,bed}"
-  - use_gff:
-      type: boolean
-      description: Specifies if feature file should be used or not
 output:
   - meta:
       type: map

modules/qualimap/bamqccram/main.nf

@@ -0,0 +1,60 @@
+process QUALIMAP_BAMQCCRAM {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.12" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:4bf11d12f2c3eccf1eb585097c0b6fd31c18c418-0' :
+        'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:4bf11d12f2c3eccf1eb585097c0b6fd31c18c418-0' }"
+
+    input:
+    tuple val(meta), path(cram), path(crai)
+    path  gff
+    path  fasta
+    path  fasta_fai
+
+    output:
+    tuple val(meta), path("${prefix}"), emit: results
+    path  "versions.yml"              , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args   ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
+
+    def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs'
+    def memory     = task.memory.toGiga() + "G"
+    def regions = gff ? "--gff $gff" : ''
+
+    def strandedness = 'non-strand-specific'
+    if (meta.strandedness == 'forward') {
+        strandedness = 'strand-specific-forward'
+    } else if (meta.strandedness == 'reverse') {
+        strandedness = 'strand-specific-reverse'
+    }
+    """
+    unset DISPLAY
+    mkdir tmp
+    export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
+
+    samtools view -hb -T ${fasta} ${cram} |
+    qualimap \\
+        --java-mem-size=$memory \\
+        bamqc \\
+        $args \\
+        -bam /dev/stdin \\
+        $regions \\
+        -p $strandedness \\
+        $collect_pairs \\
+        -outdir $prefix \\
+        -nt $task.cpus
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+}

modules/qualimap/bamqccram/meta.yml

@@ -0,0 +1,51 @@
+name: qualimap_bamqccram
+description: Evaluate alignment data
+keywords:
+  - quality control
+  - qc
+  - bam
+tools:
+  - qualimap:
+      description: |
+        Qualimap 2 is a platform-independent application written in
+        Java and R that provides both a Graphical User Interface and
+        a command-line interface to facilitate the quality control of
+        alignment sequencing data and its derivatives like feature counts.
+      homepage: http://qualimap.bioinfo.cipf.es/
+      documentation: http://qualimap.conesalab.org/doc_html/index.html
+      doi: 10.1093/bioinformatics/bts503
+      licence: ["GPL-2.0-only"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bacramm:
+      type: file
+      description: BAM file
+      pattern: "*.{bam}"
+  - gff:
+      type: file
+      description: Feature file with regions of interest
+      pattern: "*.{gff,gtf,bed}"
+  - fasta:
+      type: file
+      description: Reference file of cram file
+      pattern: "*.{fasta,fa,fna}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - results:
+      type: dir
+      description: Qualimap results dir
+      pattern: "*/*"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@FriederikeHanssen"

tests/config/pytest_modules.yml

@@ -1233,6 +1233,10 @@ qualimap/bamqc:
   - modules/qualimap/bamqc/**
   - tests/modules/qualimap/bamqc/**
 
+qualimap/bamqccram:
+  - modules/qualimap/bamqccram/**
+  - tests/modules/qualimap/bamqccram/**
+
 quast:
   - modules/quast/**
   - tests/modules/quast/**

tests/modules/qualimap/bamqc/main.nf

@@ -8,8 +8,7 @@ workflow test_qualimap_bamqc {
     input   = [ [ id:'test', single_end:false ], // meta map
                 [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
               ]
-    gff     = file("dummy_file.txt")
-    use_gff = false
+    gff     = []
 
-    QUALIMAP_BAMQC ( input, gff, use_gff )
+    QUALIMAP_BAMQC ( input, gff )
 }

tests/modules/qualimap/bamqccram/main.nf

@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { QUALIMAP_BAMQCCRAM } from '../../../../modules/qualimap/bamqccram/main.nf'
+
+workflow test_qualimap_bamqc {
+    input   = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+              ]
+    gff     = []
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    QUALIMAP_BAMQCCRAM ( input, gff, fasta, fai )
+}

tests/modules/qualimap/bamqccram/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/qualimap/bamqccram/test.yml

@@ -0,0 +1,80 @@
+- name: qualimap bamqccram test_qualimap_bamqc
+  command: nextflow run tests/modules/qualimap/bamqccram -entry test_qualimap_bamqc -c tests/config/nextflow.config
+  tags:
+    - qualimap/bamqccram
+    - qualimap
+  files:
+    - path: ./output/qualimap/test/qualimapReport.html
+    - path: ./output/qualimap/test/genome_results.txt
+      md5sum: 61d8b36507652fd7d7db9583de708161
+    - path: ./output/qualimap/test/css/plus.png
+      md5sum: 0125e6faa04e2cf0141a2d599d3bb220
+    - path: ./output/qualimap/test/css/down-pressed.png
+      md5sum: ebe8979581eda700fb234a73c661a4b9
+    - path: ./output/qualimap/test/css/underscore.js
+      md5sum: db5ba047a66617d4cd3e8c5099cc51db
+    - path: ./output/qualimap/test/css/ajax-loader.gif
+      md5sum: ae6667053ad118020b8e68ccf307b519
+    - path: ./output/qualimap/test/css/searchtools.js
+      md5sum: d550841adeedc8ed47c40ee607620937
+    - path: ./output/qualimap/test/css/up.png
+    - path: ./output/qualimap/test/css/file.png
+    - path: ./output/qualimap/test/css/up-pressed.png
+    - path: ./output/qualimap/test/css/down.png
+    - path: ./output/qualimap/test/css/minus.png
+    - path: ./output/qualimap/test/css/bgtop.png
+    - path: ./output/qualimap/test/css/comment.png
+    - path: ./output/qualimap/test/css/basic.css
+      md5sum: 25b2823342c0604924a2870eeb4e7e94
+    - path: ./output/qualimap/test/css/report.css
+      md5sum: 7a5f09eaf7c176f966f4e8854168b812
+    - path: ./output/qualimap/test/css/pygments.css
+      md5sum: d625a0adb949f181bd0d3f1432b0fa7f
+    - path: ./output/qualimap/test/css/comment-close.png
+    - path: ./output/qualimap/test/css/doctools.js
+      md5sum: 5ff571aa60e63f69c1890283e240ff8d
+    - path: ./output/qualimap/test/css/comment-bright.png
+    - path: ./output/qualimap/test/css/qualimap_logo_small.png
+    - path: ./output/qualimap/test/css/websupport.js
+      md5sum: 9e61e1e8a7433c56bd7e5a615affcf85
+    - path: ./output/qualimap/test/css/agogo.css
+      md5sum: bd757b1a7ce6fdc0288ba148680f4583
+    - path: ./output/qualimap/test/css/bgfooter.png
+    - path: ./output/qualimap/test/css/jquery.js
+      md5sum: 10092eee563dec2dca82b77d2cf5a1ae
+    - path: ./output/qualimap/test/raw_data_qualimapReport/insert_size_histogram.txt
+      md5sum: b7aeda7558e9b31f027f7dc530df90b8
+    - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt
+      md5sum: 42774c6edd6e36538acbdb6ffbd019c2
+    - path: ./output/qualimap/test/raw_data_qualimapReport/genome_fraction_coverage.txt
+      md5sum: 972a19d4846bf4e93ba32ae3dff5289c
+    - path: ./output/qualimap/test/raw_data_qualimapReport/mapping_quality_histogram.txt
+      md5sum: 4e3918da81202b52395a576f99c1a50f
+    - path: ./output/qualimap/test/raw_data_qualimapReport/insert_size_across_reference.txt
+    - path: ./output/qualimap/test/raw_data_qualimapReport/coverage_histogram.txt
+      md5sum: 353e74d2a6c4281686c9063de570a64d
+    - path: ./output/qualimap/test/raw_data_qualimapReport/mapping_quality_across_reference.txt
+      md5sum: 9bf33149528be9a0e154e4ba7cb89420
+    - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
+      md5sum: be36d9346a402ba580718497d5075d06
+    - path: ./output/qualimap/test/raw_data_qualimapReport/homopolymer_indels.txt
+      md5sum: b0e19fcfb60e5f039eb0986ef61ab3ed
+    - path: ./output/qualimap/test/raw_data_qualimapReport/duplication_rate_histogram.txt
+      md5sum: 76e80e4ce8d0e01bbd65f1c28f5a92e7
+    - path: ./output/qualimap/test/raw_data_qualimapReport/coverage_across_reference.txt
+      md5sum: b609d33a1f98d24aa84a04e60513cbee
+    - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_clipping_profile.txt
+      md5sum: 7c86f7b225b99bc60008d7e4e55d6adb
+    - path: ./output/qualimap/test/images_qualimapReport/genome_reads_content_per_read_position.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_gc_content_per_window.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_0to50_histogram.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_uniq_read_starts_histogram.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_mapping_quality_across_reference.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_histogram.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_across_reference.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_homopolymer_indels.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_insert_size_histogram.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_mapping_quality_histogram.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_insert_size_across_reference.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_reads_clipping_profile.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_quotes.png