Merge branch 'master' into nf-test_phispy

* master:
  Added contrast limited adaptive histogram equalization module (nf-core#5268)
  Leviosam2 index (nf-core#5316)
  Add subworkflow mapAD (nf-core#5239)
  Remove AMRFinderPlus DB update on each invocation (nf-core#5232)
  Revert "add paths in output directive in cellranger cout module" (nf-core#5306)
  Revert "update kallistobustools count output list" (nf-core#5307)
  Igv reports (nf-core#5263)
  Remove unnecessary .view() in subworkflows/nf-core/vcf_phase_shapeit5 & tests/modules/nf-core/shapeit5/ligate/main.nf (nf-core#5280)
  Add wittyer as module (nf-core#5171)
  Bamstats (nf-core#4474)
  gatk4_asereadcounter add updated meta and nf-tests (nf-core#5164)
  4557 new module kaijumergeoutputs + stub Kraken2/Kraken2 (nf-core#5249)
  add cram/index support to bwamem2 (nf-core#5248)
  Add README to modules build with Docker (nf-core#4935)
  update paths for VEP (nf-core#5281)
  nf-test bases2fastq (nf-core#5272)
  Add module seqfu/stats (nf-core#5275)
  Added gt/gff3validator (nf-core#4718)
  Added liftoff (nf-core#5209)

.github/workflows/test.yml

@@ -561,6 +561,8 @@ jobs:
             tags: merquryfk/merquryfk
           - profile: conda
             tags: merquryfk/ploidyplot
+          - profile: conda
+            tags: molkartgarage/clahe
           - profile: conda
             tags: quartonotebook
           - profile: conda
@@ -585,6 +587,8 @@ jobs:
             tags: subworkflows/vcf_annotate_ensemblvep
           - profile: singularity
             tags: bases2fastq
+          - profile: conda
+            tags: wittyer
     env:
       NXF_ANSI_LOG: false
       SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}

modules/nf-core/bakta/bakta/main.nf

@@ -35,8 +35,6 @@ process BAKTA_BAKTA {
     def proteins_opt = proteins ? "--proteins ${proteins[0]}" : ""
     def prodigal_tf = prodigal_tf ? "--prodigal-tf ${prodigal_tf[0]}" : ""
     """
-    amrfinder_update --force_update --database $db/amrfinderplus-db
-
     bakta \\
         $fasta \\
         $args \\

modules/nf-core/bamstats/generalstats/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "bamstats_generalstats"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::bamstats=0.3.5"

modules/nf-core/bamstats/generalstats/main.nf

@@ -0,0 +1,51 @@
+process BAMSTATS_GENERALSTATS {
+    tag "$meta.id"
+    label 'process_single'
+    conda "bioconda::bamstats=0.3.5"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bamstats:0.3.5--he881be0_0':
+        'biocontainers/bamstats:0.3.5--he881be0_0' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.json"), emit: json
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // Several ARGS are available.
+    //  -a is a helpfu; one where you can add a BED file
+    //  -u, --uniq outputs genomic coverage statistics for uniqely mapped reads
+    """
+    bamstats \\
+        -i $bam \\
+        $args \\
+        -c $task.cpus \\
+        -o ${prefix}.json
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bamstats: \$(echo \$(bamstats --version 2>&1) | sed 's/^.*bamstats == version://; s/Using.*\$//' | sed 's/built.*//' )
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.json
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bamstats: \$(echo \$(bamstats --version 2>&1) | sed 's/^.*bamstats == version://; s/Using.*\$//' | sed 's/built.*//' )
+    END_VERSIONS
+    """
+}
+

modules/nf-core/bamstats/generalstats/meta.yml

@@ -0,0 +1,46 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "bamstats_generalstats"
+description: write your description here
+keywords:
+  - bam
+  - statistics
+  - genomics
+tools:
+  - "bamstats":
+      description: "A command line tool to compute mapping statistics from a BAM file"
+      homepage: "https://github.com/guigolab/bamstats/"
+      documentation: "https://github.com/guigolab/bamstats/"
+      tool_dev_url: "https://github.com/guigolab"
+      licence: ["BSD-3-clause"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - json:
+      type: file
+      description: json containing bam statistics
+      pattern: "*.json"
+
+authors:
+  - "@johnoooh"

modules/nf-core/bamstats/generalstats/tests/main.nf.test

@@ -0,0 +1,60 @@
+nextflow_process {
+
+    name "Test Process BAMSTATS_GENERALSTATS"
+    script "../main.nf"
+    process "BAMSTATS_GENERALSTATS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bamstats"
+    tag "bamstats/generalstats"
+
+    test("sarscov2 - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.json.get(0)[1]).exists() },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.json.get(0)[1]).exists() },
+                { assert snapshot(process.out.versions).match("versions_stub") }
+            )
+        }
+
+    }
+
+}

modules/nf-core/bamstats/generalstats/tests/tags.yml

@@ -0,0 +1,2 @@
+bamstats/generalstats:
+  - "modules/nf-core/bamstats/generalstats/**"

modules/nf-core/bases2fastq/main.nf

@@ -41,4 +41,21 @@ process BASES2FASTQ {
         bases2fastq: \$(bases2fastq --version | sed -e "s/bases2fastq version //g")
     END_VERSIONS
     """
+
+    stub:
+    """
+    mkdir output
+    mkdir output/Samples
+    mkdir output/Samples/DefaultSample
+
+    touch output/Metrics.csv
+    touch output/RunManifest.json
+    touch output/UnassignedSequences.csv
+    echo | gzip > output/Samples/DefaultSample/DefaultSample_R1.fastq.gz
+    echo | gzip > output/Samples/DefaultSample/DefaultSample_R2.fastq.gz
+    touch output/Bases2Fastq-Sim_QC.html
+    touch output/RunStats.json
+    touch output/Samples/DefaultSample/DefaultSample_stats.json
+    touch versions.yml
+    """
 }

modules/nf-core/bases2fastq/tests/main.nf.test

@@ -0,0 +1,78 @@
+nextflow_process {
+
+    name "Test Process BASES2FASTQ"
+    script "../main.nf"
+    process "BASES2FASTQ"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bases2fastq"
+    tag "untar"
+
+    setup {
+        run("UNTAR") {
+            script "modules/nf-core/untar/main.nf"
+            process {
+                """
+                input[0] = Channel.of([ [id: "sim-data",  samplesheet: file("https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/sim-data/RunManifest.csv", checkIfExists: true)], file("https://github.com/nf-core/test-datasets/raw/demultiplex/testdata/sim-data/sim-data.tar.gz", checkIfExists: true) ])
+                """
+            }
+        }
+    }
+
+    test("sim-data.tar.gz - bcl") {
+        when {
+            process {
+                """
+                input[0]= UNTAR.out.untar.map{meta, untar -> [meta, meta.samplesheet, untar]}
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.metrics,
+                    process.out.generated_run_manifest,
+                    process.out.unassigned,
+                    process.out.sample_fastq,
+                    file(process.out.qc_report[0][1]).name,
+                    file(process.out.run_stats[0][1]).name,
+                    file(process.out.sample_json[0][1]).name
+                    ).match() 
+                }
+            )
+        }
+
+    }
+
+    test("sim-data.tar.gz - bcl -stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0]= UNTAR.out.untar.map{meta, untar -> [meta, meta.samplesheet, untar]}
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.metrics,
+                    process.out.generated_run_manifest,
+                    process.out.unassigned,
+                    process.out.sample_fastq,
+                    file(process.out.qc_report[0][1]).name,
+                    file(process.out.run_stats[0][1]).name,
+                    file(process.out.sample_json[0][1]).name
+                    ).match() 
+                }
+            )
+        }
+    }
+}