Merge remote-tracking branch 'origin/nftest_haplotyper' into nftest_h…

…aplotyper
nf-core · Jul 31, 2024 · 4e983df · 4e983df
2 parents 66a0bb4 + 49d8cfd
commit 4e983df
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diff --git a/modules/nf-core/antismash/antismashlite/tests/main.nf.test b/modules/nf-core/antismash/antismashlite/tests/main.nf.test
@@ -66,7 +66,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz', checkIfExists: true)
                 ]
                 """
             }

diff --git a/modules/nf-core/bclconvert/tests/main.nf.test b/modules/nf-core/bclconvert/tests/main.nf.test
@@ -15,8 +15,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id: 'test', lane:1 ],
-                    file(params.test_data['homo_sapiens']['illumina']['test_flowcell_samplesheet'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bcl/flowcell_samplesheet.csv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz', checkIfExists: true)
                 ]
                 """
             }

diff --git a/modules/nf-core/bedops/convert2bed/tests/main.nf.test b/modules/nf-core/bedops/convert2bed/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
                     ]
                 """
             }
@@ -41,7 +41,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
                     ]
                 """
             }

diff --git a/modules/nf-core/bedops/gtf2bed/tests/main.nf.test b/modules/nf-core/bedops/gtf2bed/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [[ id:'test' ], // meta map
-                             file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+                             file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)
                 ]
                 """
             }
@@ -38,7 +38,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [[ id:'test' ], // meta map
-                             file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+                             file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)
                 ]
                 """
             }

diff --git a/modules/nf-core/biscuit/align/tests/main.nf.test b/modules/nf-core/biscuit/align/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
             script "../../index/main.nf"
             process {
             """
-            input[0] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+            input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
             """
         }
         }
@@ -28,7 +28,7 @@ nextflow_process {
                 """
                 input[0] = [
                             [ id:'test' ], // meta map
-                            [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true) ]
+                            [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) ]
                 ]
                 input[1] = BISCUIT_INDEX.out.index
                 """
@@ -52,8 +52,8 @@ nextflow_process {
                 """
                 input[0] = [
                             [ id:'test' ], // meta map
-                            [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
-                              file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
+                            [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true),
+                              file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) ]
                 ]
                 input[1] = BISCUIT_INDEX.out.index
                 """

diff --git a/modules/nf-core/biscuit/bsconv/tests/main.nf.test b/modules/nf-core/biscuit/bsconv/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
             script "../../index/main.nf"
             process {
             """
-            input[0] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+            input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
             """
             }
         }
@@ -27,8 +27,8 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [id:'test', single_end:false ], // meta map
-                            file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
-                            file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true)
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true)
                             ]
 
                 input[1] = BISCUIT_INDEX.out.index
@@ -54,8 +54,8 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [id:'test', single_end:false ], // meta map
-                            file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
-                            file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true)
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true)
                             ]
 
                 input[1] = BISCUIT_INDEX.out.index

diff --git a/modules/nf-core/checkqc/environment.yml b/modules/nf-core/checkqc/environment.yml
@@ -5,7 +5,8 @@ channels:
   - defaults
 dependencies:
   - python=3.8
+  - numpy=1.26
   - pip
   - pip: # FIXME https://github.com/nf-core/modules/issues/5814
-      - checkqc==3.8.0
-      - interop==1.2.4
+      - checkqc==4.0.3
+      - interop==1.3.2
diff --git a/modules/nf-core/checkqc/main.nf b/modules/nf-core/checkqc/main.nf
@@ -2,14 +2,15 @@ process CHECKQC {
     tag "$meta.id"
     label 'process_single'
 
-    container "community.wave.seqera.io/library/python_pip_interop_checkqc:d76c912c8fadc561"
+    container "community.wave.seqera.io/library/python_numpy_pip_checkqc_interop:b5301d9801b8e66b"
 
     input:
     tuple val(meta), path(run_dir)
     path(checkqc_config)
 
     output:
     tuple val(meta), path("*checkqc_report.json"), emit: report
+    tuple val(meta), path("*checkqc_log.txt")    , emit: log
     path "versions.yml"                          , emit: versions
 
     when:
@@ -29,7 +30,13 @@ process CHECKQC {
         $args \
         $config \
         --json \
-        $run_dir > checkqc_report.json
+        $run_dir > checkqc_report.json 2> checkqc_log.txt || true
+
+    # Check if the output JSON file is empty
+    if [[ ! -s checkqc_report.json ]] ; then
+        echo "Error: Empty JSON files. Most likely due to missing files in run directory. See checkQC log file for errors."
+        exit 1
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/checkqc/meta.yml b/modules/nf-core/checkqc/meta.yml
@@ -34,6 +34,10 @@ output:
       type: file
       description: CheckQC report in json format
       pattern: "*checkqc_report.json"
+  - log:
+      type: file
+      description: CheckQC log in txt format
+      pattern: "*_log.txt"
 
 authors:
   - "@matrulda"
diff --git a/modules/nf-core/checkqc/tests/main.nf.test b/modules/nf-core/checkqc/tests/main.nf.test
@@ -34,7 +34,81 @@ nextflow_process {
         then {
             assertAll(
             { assert process.success },
-            { assert snapshot(process.out).match() }
+            { assert snapshot(process.out).match() },
+            { assert process.out.report },
+            { assert process.out.report.size() == 1 },
+            { assert process.out.report.get(0).get(1) ==~ ".*/checkqc_report.json" },
+            { assert path(process.out.report.get(0).get(1)).json.exit_status == 0 },
+            { assert process.out.log },
+            { assert path(process.out.log.get(0).get(1)).getText().contains("Instrument and reagent version: hiseq2500_rapidhighoutput_v4") }
+
+          )
+        }
+
+    }
+    test("homo_sapiens illumina test_miseq_noRunParameters - Log Error: no File") {
+        config "./nextflow.config"
+
+        setup {
+            run("UNTAR") {
+                script "../../untar/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([[id: 'test_no_xml'], file('https://github.com/nf-core/test-datasets/raw/demultiplex/testdata/MiSeq/220422_M11111_0222_000000000-K9H97.tar.gz', checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                    input[0] = UNTAR.out.untar
+                    input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.failed }
+          )
+        }
+
+    }
+
+    test("homo_sapiens illumina test_interop_bcl2fastqstats_flowcell - QC Error") {
+
+        setup {
+            run("UNTAR") {
+                script "../../untar/main.nf"
+                process {
+                    """
+                   input[0] = Channel.of([[id: 'test_no_downgrade_errors'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/interop_bcl2fastqstats/test_flowcell_stats.tar.gz', checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                    input[0] = UNTAR.out.untar
+                    input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() },
+            { assert process.out.report },
+            { assert process.out.report.size() == 1 },
+            { assert process.out.report.get(0).get(1) ==~ ".*/checkqc_report.json" },
+            { assert path(process.out.report.get(0).get(1)).json.exit_status == 1 },
+            { assert process.out.log },
+            { assert path(process.out.log.get(0).get(1)).getText().contains("ERROR    Fatal QC error") }
           )
         }
 

diff --git a/modules/nf-core/checkqc/tests/main.nf.test.snap b/modules/nf-core/checkqc/tests/main.nf.test.snap
@@ -1,4 +1,53 @@
 {
+    "homo_sapiens illumina test_interop_bcl2fastqstats_flowcell - QC Error": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_no_downgrade_errors"
+                        },
+                        "checkqc_report.json:md5,c0c5655b8f09d848de97f79073b2eae0"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test_no_downgrade_errors"
+                        },
+                        "checkqc_log.txt:md5,687d57a112fda6f56755d45e5c9cd0be"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,7c921c68a4de1cc3345edb1fd88444d1"
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test_no_downgrade_errors"
+                        },
+                        "checkqc_log.txt:md5,687d57a112fda6f56755d45e5c9cd0be"
+                    ]
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "test_no_downgrade_errors"
+                        },
+                        "checkqc_report.json:md5,c0c5655b8f09d848de97f79073b2eae0"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7c921c68a4de1cc3345edb1fd88444d1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-29T15:12:42.632194365"
+    },
     "homo_sapiens illumina test_interop_bcl2fastqstats_flowcell - QC OK": {
         "content": [
             {
@@ -7,29 +56,45 @@
                         {
                             "id": "test"
                         },
-                        "checkqc_report.json:md5,c69cb912a8c5bf53544764bd5bd73ae5"
+                        "checkqc_report.json:md5,7e3ac9ce7163436cbd5f5420ca08ffcd"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,c37381fc450f4ed00da2987430db8177"
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "checkqc_log.txt:md5,3e196f53b93d614580436bc574daea45"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,7c921c68a4de1cc3345edb1fd88444d1"
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "checkqc_log.txt:md5,3e196f53b93d614580436bc574daea45"
+                    ]
                 ],
                 "report": [
                     [
                         {
                             "id": "test"
                         },
-                        "checkqc_report.json:md5,c69cb912a8c5bf53544764bd5bd73ae5"
+                        "checkqc_report.json:md5,7e3ac9ce7163436cbd5f5420ca08ffcd"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c37381fc450f4ed00da2987430db8177"
+                    "versions.yml:md5,7c921c68a4de1cc3345edb1fd88444d1"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.3"
         },
-        "timestamp": "2024-07-17T18:30:52.712542733"
+        "timestamp": "2024-07-29T15:12:10.423534926"
     }
 }